Modulating lignin in plants

ABSTRACT

Materials and methods for modulating (e.g., increasing or decreasing) lignin content in plants are disclosed. For example, nucleic acids encoding lignin-modulating polypeptides are disclosed as well as methods for using such nucleic acids to generate transgenic plants having a modulated lignin content.

CROSS-REFERENCE TO RELATED APPLICATION

This application is a National Stage application under 35 U.S.C. §371 and claims the benefit under 35 U.S.C. §119(a) of International Application No. PCT/US2007/022737, having an International Filing Date of Oct. 26, 2007, which claims the benefit of priority of the U.S. Provisional Application Ser. No. 60/855,108, having a filing date of Oct. 27, 2006, all of which are incorporated herein in their entirety.

STATEMENT AS TO FEDERALLY SPONSORED RESEARCH

Funding for the work described herein was provided by the federal government (U.S. Department of Energy Grant No. DE-FG02-05ER64111), which has certain rights in the invention.

INCORPORATION-BY-REFERENCE OF SEQUENCE LISTING

The material on the accompanying diskette is hereby incorporated by reference into this application. The accompanying compact discs contain one file, 11696-232WO1—Sequence.txt, which was created on Oct. 25, 2007. The file named 11696-232WO1—Sequence.txt is 3,471 KB. The file can be accessed using Microsoft Word on a computer that uses Windows OS.

TECHNICAL FIELD

This document relates to methods and materials involved in modulating (e.g., increasing or decreasing) lignin content in plants. For example, this document provides plants having a decreased amount of lignin as well as materials and methods for making plants having a decreased amount of lignin.

BACKGROUND

Phenylpropanoids are plant-derived organic compounds that are biosynthesized from the amino acid phenylalanine. Intermediates and end products of this pathway include compounds having important roles in plants, such as phytoalexins, antiherbivory compounds, antioxidants, ultra-violet protectants, pigments, and aroma compounds. The majority of the carbon in the pathway, however, is channeled toward the synthesis of lignin. As the second most abundant polymer on earth, exceeded only by cellulose, lignin is a major carbon sink in the biosphere, accounting for about 30% of the carbon sequestered into terrestrial plant material each year (Battle et al., Science, 287:2467 (2000)).

Lignin is a major structural component of secondarily thickened cell walls of tissues with conducting and/or mechanical functions. Angiosperm lignin is composed of three main units named p-hydroxyphenyl (H), guaiacyl (G), and syringyl (S) units. These components originate from the polymerization of three monolignols, p-coumaryl, coniferyl, and sinapyl alcohols, respectively. The monolignols are synthesized from phenylalanine through successive deamination, reduction, hydroxylation, and methylation steps. The proportions of H, G, and S units in the cell wall vary according to plant species and tissue type.

As a major polymer of cell walls, lignin has a direct impact on the characteristics of plants and plant products, such as wood. Highly lignified wood is durable and therefore a good raw material for many applications. Since lignin yields more energy when burned than cellulose, lignified wood is also an excellent fuel. The mechanical support provided by lignin prevents lodging, a problem in many agronomically important plants. On the other hand, lignin is detrimental to paper manufacture and must be removed from pulp before paper can be manufactured. This is costly both in terms of energy and the environment.

Lignin also makes it difficult to break down biomass for conversion into cellulosic ethanol biofuel. Cellulosic ethanol, which exhibits a net energy content three times higher than corn ethanol, can be produced from a wide variety of cellulosic biomass feedstocks including agricultural plant wastes, plant wastes from industrial processes and energy crops grown specifically for fuel production. Cellulosic biomass is composed largely of cellulose, hemicellulose and lignin, with smaller amounts of proteins, lipids and ash. Processing cellulosic biomass aims to extract fermentable sugars from the feedstock, which requires disruption of the hemicellulose/lignin sheath that surrounds the cellulose in plant material. Technological developments that increase the yield and drive down the production cost of cellulosic ethanol can help to reduce our oil dependency in a sustainable way. Given the role of lignin in the recalcitrance of biomass for conversion to biobased fuels, in addition to the many other roles of lignin, it is desirable to have the ability to produce plants with modulated levels of lignin.

SUMMARY

This document provides methods and materials related to plants having a modulated (e.g., increased or decreased) lignin content. For example, this document provides transgenic plants such as trees having increased amounts of lignin in thickened secondary cell walls for carbon sequestration, and biomass energy crops having decreased lignin for improved conversion efficiency to ethanol. Nucleic acids used to generate transgenic plants and plant cells having a modulated lignin content, and methods for making plants and plant cells having a modulated lignin content are also provided. Transgenic plants described herein can have modulated, e.g., increased or decreased, amounts and/or rates of biosynthesis of lignin. In addition, the structure and/or composition of lignin produced by such plants can vary from that produced by corresponding wild-type plants.

Reducing the lignin content in dedicated energy crops such as switchgrass can improve the yield and facilitate the production of ethanol from cellulosic feedstock. Reducing lignin in forage crops such as alfalfa can improve the quality and digestibility of such crops. In trees, a reduction in lignin content can improve paper pulp production. Increasing the lignin content in plants can also be useful. For example, increasing lignin in plants can enhance long-term carbon sequestration in plant biomass, which, in turn, may reduce atmospheric carbon dioxide and global warming. An increased lignin content can also prevent plant lodging, make vegetables more firm and crunchy, enhance the fiber content of foodstuffs, confer plants with improved pathogen resistance, and increase the amount of energy that can be obtained by burning wood.

In one aspect, a plant cell is provided. The plant cell comprises an exogenous nucleic acid comprising a regulatory region operably linked to a polynucleotide encoding a lignin-modulating polypeptide comprising an amino acid sequence having 80% or greater sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NO:96, SEQ ID NOs:98-107, SEQ ID NOs:109-111, SEQ ID NOs:113-114, SEQ ID NOs:116-124, SEQ ID NOs:126-127, SEQ ID NOs:129-130, SEQ ID NO:132, SEQ ID NO:134, SEQ ID NO:136, SEQ ID NO:138, SEQ ID NO:140, SEQ ID NOs:142-143, SEQ ED NOs:145-147, SEQ ID NOs:149-150, SEQ ID NOs:152-156, SEQ ID NO:158, SEQ ID NOs:160-163, SEQ ID NO:165, SEQ ID NOs:167-174, SEQ ID NOs:176-181, SEQ ID NO:183, SEQ ID NO:185, SEQ ID NOs:187-188, SEQ ID NO:190, SEQ ID NOs:192-194, SEQ ID NOs:196-197, SEQ ID NO:199, SEQ ID NOs:201-202, SEQ ID NO:204, SEQ ID NO:206, SEQ ID NO:208, SEQ ID NOs:210-214, SEQ ID NO:216, SEQ ID NOs:218-220, SEQ ID NO:222, SEQ ID NO:224, SEQ ID NOs:226-227, SEQ ID NO:229, SEQ ID NO:231, SEQ ID NOs:233-238, SEQ ID NO:240, SEQ ID NO:242, SEQ ID NO:244, SEQ ID NO:246, SEQ ID NO:248, SEQ ID NO:250, SEQ ID NO:252, SEQ ID NO:254, SEQ ID NOs:256-268, SEQ ID NOs:270-279, SEQ ID NOs:281-282, SEQ ID NO:284, SEQ ID NOs:286-287, SEQ ID NO:289, SEQ ID NOs:291-298, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NOs:304-309, SEQ ID NOs:311-319, SEQ ID NOs:321-330, SEQ ID NOs:332-340, SEQ ID NO:342, SEQ ID NO:344, SEQ ID NOs:355-356, SEQ ID NOs:358-369, SEQ ID NO:371, SEQ ID NOs:373-385, SEQ ID NOs:387-388, SEQ ID NOs:390-395, SEQ ID NO:397, SEQ ID NO:399, SEQ ID NOs:401-407, SEQ ID NOs:409-463, SEQ ID NOs:465-496, SEQ ID NOs:498-500, SEQ ID NOs:502-503, SEQ ID NO:505, SEQ ID NOs:507-511, SEQ ID NOs:513-540, SEQ ID NO:542, SEQ ID NOs:544-577, SEQ ID NOs:579-581, SEQ ID NO:583, SEQ ID NO:585-587, SEQ ID NOs:589-590, SEQ ID NO:592, SEQ ID NOs:594-599, SEQ ID NOs:601-617, SEQ ID NO:619, SEQ ID NOs:621-638, SEQ ID NOs:640-672, SEQ ID NO:674, SEQ ID NOs:676-678, SEQ ID NO:680, SEQ ID NOs:682-685, SEQ ID NO:687, SEQ ID NO:689, SEQ ID NOs:691-714, SEQ ID NOs:716-717, SEQ ID NOs:719-737, SEQ ID NO:739, SEQ ID NOs:741-766, SEQ ID NO:768, SEQ ID NOs:770-776, SEQ ID NO:778, SEQ ID NOs:780-786, SEQ ID NOs:788-792, SEQ ID NO:794-807, and SEQ ID NOs:809-820; where a tissue of a plant produced from the plant cell has a difference in lignin content as compared to the corresponding lignin content in tissue of a control plant that does not comprise the nucleic acid.

The sequence identity can be 85% or greater, 90% or greater, or 95% or greater. The difference can be an increased lignin content. The difference can be a difference in the chemical composition of lignin. The difference can be a decreased lignin content. The plant cell can be capable of producing one or more lignin monomers. The plant can be from a genus selected from the group consisting of Agrostis, Avena, Festuca, Hordeum, Lolium, Medicago, Milium, Miscanthus, Panicum, Poa, Saccharum, Sorghum, Trifolium, Triticum, and Zea. The plant can be a species selected from Miscanthus hybrid (Miscanthus×giganteus), Miscanthus sinensis, Miscanthus sacchariflorus, Panicum virgatum, Populus balsamifera, and Saccharum spp.

The polypeptide sequence can be selected from the group consisting of a polypeptide having 80% or greater sequence identity to SEQ ID NOs:98-107, SEQ ID NOs:109-111, SEQ ID NOs:113-114, SEQ ID NOs:116-124, SEQ ID NOs:160-163, SEQ ID NO:165, SEQ ID NOs:167-174, SEQ ID NOs:218-220, SEQ ID NO:240, SEQ ID NO:242, SEQ ID NO:244, SEQ ID NO:246, SEQ ID NO:248, SEQ ID NO:250, SEQ ID NO:252, SEQ ID NO:254, SEQ ID NOs:256-268, SEQ ID NOs:270-279, SEQ ID NO:281-282, SEQ ID NO:344, SEQ ID NOs:378-379, SEQ ID NOs:382-383, SEQ ID NO:388, SEQ ID NOs:390-391, SEQ ID NO:393, SEQ ID NO:397, SEQ ID NO:402, SEQ ID NO:407, SEQ ID NOs:409-414, SEQ ID NO:416, SEQ ID NOs:418-420, SEQ ID NOs:423-424, SEQ ID NO:426, SEQ ID NO:430, SEQ ID NO:436, SEQ ID NO:443, SEQ ID NOs:447-452, SEQ ID NO:454, SEQ ID NO:456, SEQ ID NO:458, SEQ ID NOs:461-462, SEQ ID NOs:465-466, SEQ ID NOs:468-469, SEQ ID NOs:471-472, SEQ ID NOs:474-475, SEQ ID NOs:477-478, SEQ ID NOs:484-486, SEQ ID NO:488, SEQ ID NOs:770-776, SEQ ID NO:778, SEQ ID NOs:780-781, and SEQ ID NO:783.

The polynucleotide can be transcribed into an interfering RNA effective for inhibiting expression of a polypeptide selected from the group consisting of a polypeptide having 80% or greater sequence identity to SEQ ID NO:96, SEQ ID NOs:126-127, SEQ ID NOs:129-130, SEQ ID NO:132, SEQ ID NO:134, SEQ ID NO:136, SEQ ID NO:138, SEQ ID NO:140, SEQ ID NOs:142-143, SEQ ID NOs:145-147, SEQ ID NOs:149-150, SEQ ID NOs:152-156, SEQ ID NO:158, SEQ ID NOs:176-181, SEQ ID NO:183, SEQ ID NO:185, SEQ ID NOs:187-188, SEQ ID NO:190, SEQ ID NOs:192-194, SEQ ID NOs:196-197, SEQ ID NO:199, SEQ ID NOs:201-202, SEQ ID NO:204, SEQ ID NO:206, SEQ ID NO:208, SEQ ID NOs:210-214, SEQ ID NO:216, SEQ ID NO:222, SEQ ID NO:224, SEQ ID NO:226-227, SEQ ID NO:229, SEQ ID NO:231, SEQ ID NOs:233-238, SEQ ID NO:284, SEQ ID NOs:286-287, SEQ ID NO:289, SEQ ID NOs:291-298, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NO:304-309, SEQ ID NO:311-319, SEQ ID NO:321-330, SEQ ID NO:332-340, SEQ ID NO:342, SEQ ID NOs:355-356, SEQ ID NOs:358-369, SEQ ID NO:371, SEQ ID NOs:373-377, SEQ ID NO:492-496, SEQ ID NOs:498-500, SEQ ID NOs:502-503, SEQ ID NO:505, SEQ ID NOs:507-511, SEQ ID NOs:513-540, SEQ ID NO:542, SEQ ID NOs:544-577, SEQ ID NOs:579-581, SEQ ID NO:583, SEQ ID NO:585-587, SEQ ID NOs:589-590, SEQ ID NO:592, SEQ ID NOs:594-599, SEQ ID NOs:601-617, SEQ ID NO:619, SEQ ID NOs:621-638, SEQ ID NOs:640-672, SEQ ID NO:674, SEQ ID NOs:676-678, SEQ ID NO:680, SEQ ID NOs:682-685, SEQ ID NO:687, SEQ ID NO:689, SEQ ID NOs:691-714, SEQ ID NOs:716-717, SEQ ID NOs:719-737, SEQ ID NO:739, SEQ ID NOs:741-766, SEQ ID NOs:788-792, SEQ ID NO:794-807, and SEQ ID NOs:809-820.

The regulatory region can be a promoter. The promoter can be a lignin or cellulose biosynthesis promoter. The promoter can be selected from the group consisting of SEQ ID NOs:345-354. The promoter can be a tissue-preferential promoter. The tissue can be secondary cell wall, vascular, stem, pith, xylem, phloem, root, tuber, or leaf tissue. The promoter can be a cell type-preferential promoter. The cell can be a sieve, laticifer, companion, sclerenchyma, or xylem cell. The promoter can be an inducible promoter. The plant cell can be capable of producing one or more lignin monomers.

The plant can be from a genus selected from the group consisting of Eucalyptus, Hordeum, Medicago, Miscanthus, Oryza, Panicum, Pinus, Populus, Prunus, Quercus, Saccharum, Sorghum, Trifolium, Triticum, and Zea. The plant can be a species selected from Miscanthus hybrid (Miscanthus×giganteus), Miscanthus sinensis, Miscanthus sacchariflorus, Panicum virgatum, Populus balsamifera, and Saccharum spp.

The cell can further comprise a nucleic acid encoding a second lignin-modulating polypeptide operably linked to a second regulatory region. The nucleic acid encoding a second lignin-modulating polypeptide operably linked to a second regulatory region can be present on a second recombinant nucleic acid construct.

In another aspect, a plant is provided. The plant comprises any of the plant cells described above. Progeny of the plant also are provided, where the progeny have a difference in lignin content as compared to the corresponding lignin content in tissue of a control plant that does not comprise the nucleic acid.

In another aspect, a plant cell is provided. The plant cell comprises an exogenous nucleic acid, the exogenous nucleic acid comprising a regulatory region operably linked to a polynucleotide whose transcription product is at least 30 nucleotides in length and is complementary to a nucleic acid encoding a lignin-modulating polypeptide, the lignin-modulating polypeptide selected from the group consisting of a polypeptide having 80% or greater sequence identity to SEQ ID NO:96, SEQ ID NOs:98-107, SEQ ID NOs:109-111, SEQ ID NOs:113-114, SEQ ID NOs:116-124, SEQ ID NOs:126-127, SEQ ID NOs:129-130, SEQ ID NO:132, SEQ ID NO:134, SEQ ID NO:136, SEQ ID NO:138, SEQ ID NO:140, SEQ ID NOs:142-143, SEQ ID NOs:145-147, SEQ ID NOs:149-150, SEQ ID NOs:152-156, SEQ ID NO:158, SEQ ID NOs:160-163, SEQ ID NO:165, SEQ ID NOs:167-174, SEQ ID NOs:176-181, SEQ ID NO:183, SEQ ID NO:185, SEQ ID NOs:187-188, SEQ ID NO:190, SEQ ID NOs:192-194, SEQ ID NOs:196-197, SEQ ID NO:199, SEQ ID NOs:201-202, SEQ ID NO:204, SEQ ID NO:206, SEQ ID NO:208, SEQ ID NOs:210-214, SEQ ID NO:216, SEQ ID NOs:218-220, SEQ ID NO:222, SEQ ID NO:224, SEQ ID NOs:226-227, SEQ ID NO:229, SEQ ID NO:231, SEQ ID NOs:233-238, SEQ ID NO:240, SEQ ID NO:242, SEQ ID NO:244, SEQ ID NO:246, SEQ ID NO:248, SEQ ID NO:250, SEQ ID NO:252, SEQ ID NO:254, SEQ ID NOs:256-268, SEQ ID NOs:270-279, SEQ ID NOs:281-282, SEQ ID NO:284, SEQ ID NOs:286-287, SEQ ID NO:289, SEQ ID NOs:291-298, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NOs:304-309, SEQ ID NOs:311-319, SEQ ID NOs:321-330, SEQ ID NOs:332-340, SEQ ID NO:342, SEQ ID NO:344, SEQ ID NOs:355-356, SEQ ID NOs:358-369, SEQ ID NO:371, SEQ ID NOs:373-385, SEQ ID NOs:387-388, SEQ ID NOs:390-395, SEQ ID NO:397, SEQ ID NO:399, SEQ ID NOs:401-407, SEQ ID NOs:409-463, SEQ ID NOs:465-496, SEQ ID NOs:498-500, SEQ ID NOs:502-503, SEQ ID NO:505, SEQ ID NOs:507-511, SEQ ID NOs:513-540, SEQ ID NO:542, SEQ ID NOs:544-577, SEQ ID NOs:579-581, SEQ ID NO:583, SEQ ID NOs:585-587, SEQ ID NOs:589-590, SEQ ID NO:592, SEQ ID NOs:594-599, SEQ ID NOs:601-617, SEQ ID NO:619, SEQ ID NOs:621-638, SEQ ID NOs:640-672, SEQ ID NO:674, SEQ ID NOs:676-678, SEQ ID NO:680, SEQ ID NOs:682-685, SEQ ID NO:687, SEQ ID NO:689, SEQ ID NOs:691-714, SEQ ID NOs:716-717, SEQ ID NOs:719-737, SEQ ID NO:739, SEQ ID NOs:741-766, SEQ ID NO:768, SEQ ID NOs:770-776, SEQ ID NO:778, SEQ ID NOs:780-786, SEQ ID NOs:788-792, SEQ ID NO:794-807, and SEQ ID NOs:809-820; where a tissue of a plant produced from the plant cell has a difference in lignin content as compared to the corresponding lignin content in tissue of a control plant that does not comprise the nucleic acid.

In another aspect, a plant cell is provided. The plant cell comprises an exogenous nucleic acid, the exogenous nucleic acid comprising a regulatory region operably linked to a polynucleotide that is transcribed into an interfering RNA effective for inhibiting expression of a lignin-modulating polypeptide selected from the group consisting of a polypeptide having 80% or greater sequence identity to SEQ ID NO:96, SEQ ID NOs:98-107, SEQ ID NOs:109-111, SEQ ID NOs:113-114, SEQ ID NOs:116-124, SEQ ID NOs:126-127, SEQ ID NOs:129-130, SEQ ID NO:132, SEQ ID NO:134, SEQ ID NO:136, SEQ ID NO:138, SEQ ID NO:140, SEQ ID NOs:142-143, SEQ ID NOs:145-147, SEQ ID NOs:149-150, SEQ ID NOs:152-156, SEQ ID NO:158, SEQ ID NOs:160-163, SEQ ID NO:165, SEQ ID NOs:167-174, SEQ ID NOs:176-181, SEQ ID NO:183, SEQ ID NO:185, SEQ ID NOs:187-188, SEQ ID NO:190, SEQ ID NOs:192-194, SEQ ID NOs:196-197, SEQ ID NO:199, SEQ ID NOs:201-202, SEQ ID NO:204, SEQ ID NO:206, SEQ ID NO:208, SEQ ID NOs:210-214, SEQ ID NO:216, SEQ ID NOs:218-220, SEQ ID NO:222, SEQ ID NO:224, SEQ ID NOs:226-227, SEQ ID NO:229, SEQ ID NO:231, SEQ ID NOs:233-238, SEQ ID NO:240, SEQ ID NO:242, SEQ ID NO:244, SEQ ID NO:246, SEQ ID NO:248, SEQ ID NO:250, SEQ ID NO:252, SEQ ID NO:254, SEQ ID NOs:256-268, SEQ ID NOs:270-279, SEQ ID NOs:281-282, SEQ ID NO:284, SEQ ID NOs:286-287, SEQ ID NO:289, SEQ ID NOs:291-298, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NOs:304-309, SEQ ID NOs:311-319, SEQ ID NOs:321-330, SEQ ID NOs:332-340, SEQ ID NO:342, SEQ ID NO:344, SEQ ID NOs:355-356, SEQ ID NOs:358-369, SEQ ID NO:371, SEQ ID NOs:373-385, SEQ ID NOs:387-388, SEQ ID NOs:390-395, SEQ ID NO:397, SEQ ID NO:399, SEQ ID NOs:401-407, SEQ ID NOs:409-463, SEQ ID NOs:465-496, SEQ ID NOs:498-500, SEQ ID NOs:502-503, SEQ ID NO:505, SEQ ID NOs:507-511, SEQ ID NOs:513-540, SEQ ID NO:542, SEQ ID NOs:544-577, SEQ ID NOs:579-581, SEQ ID NO:583, SEQ ID NOs:585-587, SEQ ID NOs:589-590, SEQ ID NO:592, SEQ ID NOs:594-599, SEQ ID NOs:601-617, SEQ ID NO:619, SEQ ID NOs:621-638, SEQ ID NOs:640-672, SEQ ID NO:674, SEQ ID NOs:676-678, SEQ ID NO:680, SEQ ID NOs:682-685, SEQ ID NO:687, SEQ ID NO:689, SEQ ID NOs:691-714, SEQ ID NOs:716-717, SEQ ID NOs:719-737, SEQ ID NO:739, SEQ ID NOs:741-766, SEQ ID NO:768, SEQ ID NOs:770-776, SEQ ID NO:778, SEQ ID NOs:780-786, SEQ ID NOs:788-792, SEQ ID NO:794-807, and SEQ ID NOs:809-820; where a tissue of a plant produced from the plant cell has a difference in lignin content as compared to the corresponding lignin content in tissue of a control plant that does not comprise the nucleic acid. The exogenous nucleic acid can further comprise a 3′ UTR operably linked to the polynucleotide. The polynucleotide can be transcribed into an interfering RNA comprising a stem-loop structure. The stem-loop structure can comprise an inverted repeat of the 3′ UTR.

In another aspect, a method of modulating the lignin content in a plant is provided. The method comprises introducing into a plant cell an exogenous nucleic acid comprising a regulatory region operably linked to a nucleic acid encoding a lignin-modulating polypeptide comprising a polypeptide sequence having 80% or greater sequence identity to a polypeptide sequence selected from the group consisting of SEQ ID NO:96, SEQ ID NOs:98-107, SEQ ID NOs:109-111, SEQ ID NOs:113-114, SEQ ID NOs:116-124, SEQ ID NOs:126-127, SEQ ID NOs:129-130, SEQ ID NO:132, SEQ ID NO:134, SEQ ID NO:136, SEQ ID NO:138, SEQ ID NO:140, SEQ ID NOs:142-143, SEQ ID NOs:145-147, SEQ ID NOs:149-150, SEQ ID NOs:152-156, SEQ ID NO:158, SEQ ID NOs:160-163, SEQ ID NO:165, SEQ ID NOs:167-174, SEQ ID NOs:176-181, SEQ ID NO:183, SEQ ID NO:185, SEQ ID NOs:187-188, SEQ ID NO:190, SEQ ID NOs:192-194, SEQ ID NOs:196-197, SEQ ID NO:199, SEQ ID NOs:201-202, SEQ ID NO:204, SEQ ID NO:206, SEQ ID NO:208, SEQ ID NOs:210-214, SEQ ID NO:216, SEQ ID NOs:218-220, SEQ ID NO:222, SEQ ID NO:224, SEQ ID NOs:226-227, SEQ ID NO:229, SEQ ID NO:231, SEQ ID NOs:233-238, SEQ ID NO:240, SEQ ID NO:242, SEQ ID NO:244, SEQ ID NO:246, SEQ ID NO:248, SEQ ID NO:250, SEQ ID NO:252, SEQ ID NO:254, SEQ ID NOs:256-268, SEQ ID NOs:270-279, SEQ ID NOs:281-282, SEQ ID NO:284, SEQ ID NOs:286-287, SEQ ID NO:289, SEQ ID NOs:291-298, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NOs:304-309, SEQ ID NOs:311-319, SEQ ID NOs:321-330, SEQ ID NOs:332-340, SEQ ID NO:342, SEQ ID NO:344, SEQ ID NOs:355-356, SEQ ID NOs:358-369, SEQ ID NO:371, SEQ ID NOs:373-385, SEQ ID NOs:387-388, SEQ ID NOs:390-395, SEQ ID NO:397, SEQ ID NO:399, SEQ ID NOs:401-407, SEQ ID NOs:409-463, SEQ ID NOs:465-496, SEQ ID NOs:498-500, SEQ ID NOs:502-503, SEQ ID NO:505, SEQ ID NOs:507-511, SEQ ID NOs:513-540, SEQ ID NO:542, SEQ ID NOs:544-577, SEQ ID NOs:579-581, SEQ ID NO:583, SEQ ID NOs:585-587, SEQ ID NOs:589-590, SEQ ID NO:592, SEQ ID NOs:594-599, SEQ ID NOs:601-617, SEQ ID NO:619, SEQ ID NOs:621-638, SEQ ID NOs:640-672, SEQ ID NO:674, SEQ ID NOs:676-678, SEQ ID NO:680, SEQ ID NOs:682-685, SEQ ID NO:687, SEQ ID NO:689, SEQ ID NOs:691-714, SEQ ID NOs:716-717, SEQ ID NOs:719-737, SEQ ID NO:739, SEQ ID NOs:741-766, SEQ ID NO:768, SEQ ID NOs:770-776, SEQ ID NO:778, SEQ ID NOs:780-786, SEQ ID NOs:788-792, SEQ ID NO:794-807, and SEQ ID NOs:809-820; where a tissue of a plant produced from the plant cell has a difference in lignin content as compared to the corresponding lignin content in tissue of a control plant that does not comprise the nucleic acid.

The sequence identity can be 85% or greater, 90% or greater, or 95% or greater. The difference can be an increased lignin content. The plant cell can be capable of producing one or more lignin monomers. The plant can be from a genus selected from the group consisting of Acer, Afzelia, Eucalyptus, Fraxinus, Juglans, Pinus, Populus, Prunus, Quercus, and Solanum. The plant can be a species selected from Populus balsamifera and Solanum lycopersicum. The difference can be a difference in the chemical composition of lignin. The difference can be a decreased lignin content. The regulatory region can be a promoter. The promoter can be a lignin or cellulose biosynthesis promoter. The promoter can be selected from the group consisting of SEQ ID NOs:345-354. The promoter can be a tissue-preferential promoter. The tissue can be secondary cell wall, vascular, stem, pith, xylem, phloem, root, tuber, or leaf tissue. The promoter can be a cell type-preferential promoter. The cell can be a sieve, laticifer, companion, sclerenchyma, or xylem cell. The promoter can be an inducible promoter. The cell can further comprise a nucleic acid encoding a second lignin-modulating polypeptide operably linked to a second regulatory region. The nucleic acid encoding a second lignin-modulating polypeptide operably linked to a second regulatory region can be present on a second recombinant nucleic acid construct.

In another aspect, a method of modulating the lignin content in a plant is provided. The method comprises introducing into a plant cell an exogenous nucleic acid comprising a regulatory region operably linked to a polynucleotide whose transcription product is at least 30 nucleotides in length and is complementary to a nucleic acid encoding a lignin-modulating polypeptide, the lignin-modulating polypeptide selected from the group consisting of a polypeptide having 80% or greater sequence identity to SEQ ID NO:96, SEQ ID NOs:98-107, SEQ ID NOs:109-111, SEQ ID NOs:113-114, SEQ ID NOs:116-124, SEQ ID NOs:126-127, SEQ ID NOs:129-130, SEQ ID NO:132, SEQ ID NO:134, SEQ ID NO:136, SEQ ID NO:138, SEQ ID NO:140, SEQ ID NOs:142-143, SEQ ID NOs:145-147, SEQ ID NOs:149-150, SEQ ID NOs:152-156, SEQ ID NO:158, SEQ ID NOs:160-163, SEQ ID NO:165, SEQ ID NOs:167-174, SEQ ID NOs:176-181, SEQ ID NO:183, SEQ ID NO:185, SEQ ID NOs:187-188, SEQ ID NO:190, SEQ ID NOs:192-194, SEQ ID NOs:196-197, SEQ ID NO:199, SEQ ID NOs:201-202, SEQ ID NO:204, SEQ ID NO:206, SEQ ID NO:208, SEQ ID NOs:210-214, SEQ ID NO:216, SEQ ID NOs:218-220, SEQ ID NO:222, SEQ ID NO:224, SEQ ID NOs:226-227, SEQ ID NO:229, SEQ ID NO:231, SEQ ID NOs:233-238, SEQ ID NO:240, SEQ ID NO:242, SEQ ID NO:244, SEQ ID NO:246, SEQ ID NO:248, SEQ ID NO:250, SEQ ID NO:252, SEQ ID NO:254, SEQ ID NOs:256-268, SEQ ID NOs:270-279, SEQ ID NOs:281-282, SEQ ID NO:284, SEQ ID NOs:286-287, SEQ ID NO:289, SEQ ID NOs:291-298, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NOs:304-309, SEQ ID NOs:311-319, SEQ ID NOs:321-330, SEQ ID NOs:332-340, SEQ ID NO:342, SEQ ID NO:344, SEQ ID NOs:355-356, SEQ ID NOs:358-369, SEQ ID NO:371, SEQ ID NOs:373-385, SEQ ID NOs:387-388, SEQ ID NOs:390-395, SEQ ID NO:397, SEQ ID NO:399, SEQ ID NOs:401-407, SEQ ID NOs:409-463, SEQ ID NOs:465-496, SEQ ID NOs:498-500, SEQ ID NOs:502-503, SEQ ID NO:505, SEQ ID NOs:507-511, SEQ ID NOs:513-540, SEQ ID NO:542, SEQ ID NOs:544-577, SEQ ID NOs:579-581, SEQ ID NO:583, SEQ ID NOs:585-587, SEQ ID NOs:589-590, SEQ ID NO:592, SEQ ID NOs:594-599, SEQ ID NOs:601-617, SEQ ID NO:619, SEQ ID NOs:621-638, SEQ ID NOs:640-672, SEQ ID NO:674, SEQ ID NOs:676-678, SEQ ID NO:680, SEQ ID NOs:682-685, SEQ ID NO:687, SEQ ID NO:689, SEQ ID NOs:691-714, SEQ ID NOs:716-717, SEQ ID NOs:719-737, SEQ ID NO:739, SEQ ID NOs:741-766, SEQ ID NO:768, SEQ ID NOs:770-776, SEQ ID NO:778, SEQ ID NOs:780-786, SEQ ID NOs:788-792, SEQ ID NO:794-807, and SEQ ID NOs:809-820; where a tissue of a plant produced from the plant cell has a difference in lignin content as compared to the corresponding lignin content in tissue of a control plant that does not comprise the nucleic acid.

In another aspect, a method of modulating the lignin content in a plant is provided. The method comprises introducing into a plant cell an exogenous nucleic acid comprising a regulatory region operably linked to a polynucleotide that is transcribed into an interfering RNA effective for inhibiting expression of a lignin-modulating polypeptide selected from the group consisting of a polypeptide having 80% or greater sequence identity to SEQ ID NO:96, SEQ ID NOs:98-107, SEQ ID NOs:109-111, SEQ ID NOs:113-114, SEQ ID NOs:116-124, SEQ ID NOs:126-127, SEQ ID NOs:129-130, SEQ ID NO:132, SEQ ID NO:134, SEQ ID NO:136, SEQ ID NO:138, SEQ ID NO:140, SEQ ID NOs:142-143, SEQ ID NOs:145-147, SEQ ID NOs:149-150, SEQ ID NOs:152-156, SEQ ID NO:158, SEQ ID NOs:160-163, SEQ ID NO:165, SEQ ID NOs:167-174, SEQ ID NOs:176-181, SEQ ID NO:183, SEQ ID NO:185, SEQ ID NOs:187-188, SEQ ID NO:190, SEQ ID NOs:192-194, SEQ ID NOs:196-197, SEQ ID NO:199, SEQ ID NOs:201-202, SEQ ID NO:204, SEQ ID NO:206, SEQ ID NO:208, SEQ ID NOs:210-214, SEQ ID NO:216, SEQ ID NOs:218-220, SEQ ID NO:222, SEQ ID NO:224, SEQ ID NOs:226-227, SEQ ID NO:229, SEQ ID NO:231, SEQ ID NOs:233-238, SEQ ID NO:240, SEQ ID NO:242, SEQ ID NO:244, SEQ ID NO:246, SEQ ID NO:248, SEQ ID NO:250, SEQ ID NO:252, SEQ ID NO:254, SEQ ID NOs:256-268, SEQ ID NOs:270-279, SEQ ID NOs:281-282, SEQ ID NO:284, SEQ ID NOs:286-287, SEQ ID NO:289, SEQ ID NOs:291-298, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NOs:304-309, SEQ ID NOs:311-319, SEQ ID NOs:321-330, SEQ ID NOs:332-340, SEQ ID NO:342, SEQ ID NO:344, SEQ ID NOs:355-356, SEQ ID NOs:358-369, SEQ ID NO:371, SEQ ID NOs:373-385, SEQ ID NOs:387-388, SEQ ID NOs:390-395, SEQ ID NO:397, SEQ ID NO:399, SEQ ID NOs:401-407, SEQ ID NOs:409-463, SEQ ID NOs:465-496, SEQ ID NOs:498-500, SEQ ID NOs:502-503, SEQ ID NO:505, SEQ ID NOs:507-511, SEQ ID NOs:513-540, SEQ ID NO:542, SEQ ID NOs:544-577, SEQ ID NOs:579-581, SEQ ID NO:583, SEQ ID NOs:585-587, SEQ ID NOs:589-590, SEQ ID NO:592, SEQ ID NOs:594-599, SEQ ID NOs:601-617, SEQ ID NO:619, SEQ ID NOs:621-638, SEQ ID NOs:640-672, SEQ ID NO:674, SEQ ID NOs:676-678, SEQ ID NO:680, SEQ ID NOs:682-685, SEQ ID NO:687, SEQ ID NO:689, SEQ ID NOs:691-714, SEQ ID NOs:716-717, SEQ ID NOs:719-737, SEQ ID NO:739, SEQ ID NOs:741-766, SEQ ID NO:768, SEQ ID NOs:770-776, SEQ ID NO:778, SEQ ID NOs:780-786, SEQ ID NOs:788-792, SEQ ID NO:794-807, and SEQ ID NOs:809-820; where a tissue of a plant produced from the plant cell has a difference in lignin content as compared to the corresponding lignin content in tissue of a control plant that does not comprise the nucleic acid.

The exogenous nucleic acid can further comprise a 3′ UTR operably linked to the polynucleotide. The polynucleotide can be transcribed into an interfering RNA comprising a stem-loop structure. The stem-loop structure can comprise an inverted repeat of the 3′ UTR. The difference can be a decreased lignin content. The plant can be from a genus selected from the group consisting of Agrostis, Avena, Festuca, Hordeum, Lolium, Medicago, Milium, Miscanthus, Panicum, Poa, Saccharum, Sorghum, Trifolium, Triticum, and Zea.

In another aspect, an isolated nucleic acid molecule is provided. The isolated nucleic acid molecule comprises a nucleotide sequence having 95% or greater sequence identity to the nucleotide sequence set forth in SEQ ID NO:108, SEQ ID NO:112, SEQ ID NO:115, SEQ ID NO:128, SEQ ID NO:131, SEQ ID NO:137, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:144, SEQ ID NO:151, SEQ ID NO:157, SEQ ID NO:164, SEQ ID NO:166, SEQ ID NO:184, SEQ ID NO:186, SEQ ID NO:198, SEQ ID NO:200, SEQ ID NO:205, SEQ ID NO:207, SEQ ID NO:209, SEQ ID NO:223, SEQ ID NO:228, SEQ ID NO:230, SEQ ID NO:232, SEQ ID NO:241, SEQ ID NO:243, SEQ ID NO:245, SEQ ID NO:247, SEQ ID NO:249, SEQ ID NO:251, SEQ ID NO:253, SEQ ID NO:255, SEQ ID NO:269, SEQ ID NO:299, SEQ ID NO:301, SEQ ID NO:303, SEQ ID NO:310, SEQ ID NO:320, SEQ ID NO:331, SEQ ID NO:341, SEQ ID NO:343, SEQ ID NO:357, SEQ ID NO:370, SEQ ID NO:386, SEQ ID NO:389, SEQ ID NO:396, SEQ ID NO:398, SEQ ID NO:400, SEQ ID NO:408, SEQ ID NO:464, SEQ ID NO:497, SEQ ID NO:501, SEQ ID NO:504, SEQ ID NO:506, SEQ ID NO:512, SEQ ID NO:541, SEQ ID NO:578, SEQ ID NO:582, SEQ ID NO:584, SEQ ID NO:591, SEQ ID NO:593, SEQ ID NO:600, SEQ ID NO:618, SEQ ID NO:639, SEQ ID NO:673, SEQ ID NO:675, SEQ ID NO:679, SEQ ID NO:681, SEQ ID NO:688, SEQ ID NO:690, SEQ ID NO:715, SEQ ID NO:738, SEQ ID NO:740, SEQ ID NO:767, SEQ ID NO:769, SEQ ID NO:779, SEQ ID NO:787, SEQ ID NO:793, or SEQ ID NO:808.

In another aspect, an isolated nucleic acid is provided. The isolated nucleic acid comprises a nucleotide sequence encoding a polypeptide having 80% or greater sequence identity to the amino acid sequence set forth in SEQ ID NO:109, SEQ ID NO:113, SEQ ID NO:116, SEQ ID NO:129, SEQ ID NO:132, SEQ ID NO:138, SEQ ID NO:140, SEQ ID NO:142, SEQ ID NO:145, SEQ ID NO:152, SEQ ID NO:158, SEQ ID NO:165, SEQ ID NO:167, SEQ ID NO:185, SEQ ID NO:187, SEQ ID NO:199, SEQ ID NO:201, SEQ ID NO:206, SEQ ID NO:208, SEQ ID NO:210, SEQ ID NO:224, SEQ ID NO:229, SEQ ID NO:231, SEQ ID NO:233, SEQ ID NO:242, SEQ ID NO:244, SEQ ID NO:246, SEQ ID NO:248, SEQ ID NO:250, SEQ ID NO:252, SEQ ID NO:254, SEQ ID NO:256, SEQ ID NO:270, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NO:304, SEQ ID NO:311, SEQ ID NO:321, SEQ ID NO:332, SEQ ID NO:342, SEQ ID NO:344, SEQ ID NO:358, SEQ ID NO:371, SEQ ID NO:389, SEQ ID NO:390, SEQ ID NO:397, SEQ ID NO:399, SEQ ID NO:401, SEQ ID NO:409, SEQ ID NO:465, SEQ ID NO:498, SEQ ID NO:502, SEQ ID NO:505, SEQ ID NO:507, SEQ ID NO:513, SEQ ID NO:542, SEQ ID NO:579, SEQ ID NO:583, SEQ ID NO:585, SEQ ID NO:592, SEQ ID NO:594, SEQ ID NO:601, SEQ ID NO:619, SEQ ID NO:640, SEQ ID NO:674, SEQ ID NO:676, SEQ ID NO:680, SEQ ID NO:682, SEQ ID NO:689, SEQ ID NO:691, SEQ ID NO:716, SEQ ID NO:739, SEQ ID NO:741, SEQ ID NO:768, SEQ ID NO:770, SEQ ID NO:780, SEQ ID NO:788, SEQ ID NO:794, or SEQ ID NO:809.

In yet another aspect, a method of producing a plant is provided. The method comprises growing a plant cell comprising an exogenous nucleic acid. The exogenous nucleic acid comprises a regulatory region operably linked to a nucleotide sequence encoding a polypeptide. The Hidden Markov Model (HMM) bit score of the amino acid sequence of the polypeptide is greater than about 20, using an HMM generated from the amino acid sequences depicted in one of FIGS. 1 to 22. The plant has a difference in lignin content as compared to the corresponding lignin content of a control plant that does not comprise said nucleic acid.

Methods of modulating the level of lignin in a plant are provided herein. In one aspect, a method comprises introducing into a plant cell an exogenous nucleic acid, said exogenous nucleic acid comprising a regulatory region operably linked to a nucleotide sequence encoding a polypeptide, wherein the HMM bit score of the amino acid sequence of said polypeptide is greater than about 20, said HMM based on the amino acid sequences depicted in one of FIGS. 1 to 22, and wherein a tissue of a plant produced from said plant cell has a difference in the lignin content as compared to the corresponding lignin content of a control plant that does not comprise said exogenous nucleic acid.

Plant cells comprising an exogenous nucleic acid are provided herein. The exogenous nucleic acid comprises a regulatory region operably linked to a nucleotide sequence encoding a polypeptide. The HMM bit score of the amino acid sequence of the polypeptide is greater than about 20, using an HMM generated from the amino acid sequences depicted in one of FIGS. 1 to 22. A tissue of a plant produced from the plant cell has a difference in lignin content as compared to the corresponding lignin content of a control plant that does not comprise the nucleic acid. A transgenic plant comprising such a plant cell also is provided.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention pertains. Although methods and materials similar or equivalent to those described herein can be used to practice the invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

The details of one or more embodiments of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the description and drawings, and from the claims.

DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1F are an alignment of the amino acid sequence of Annot ID 535161 (SEQ ID NO:98) with homologous and/or orthologous amino acid sequences gi|10197650 (SEQ ID NO:101), gi|47933890 (SEQ ID NO:105), gi|85001689 (SEQ ID NO:106), gi|5731998 (SEQ ID NO:107), CeresAnnot:1487764 (SEQ ID NO:109), gi|77744233 (SEQ ID NO:110), gi|46403211 (SEQ ID NO:117), gi|92888952 (SEQ ID NO:118), gi|57470997 (SEQ ID NO:119), gi|5002354 (SEQ ID NO:120), CeresClone:1585325 (SEQ ID NO:121), gi|110289397 (SEQ ID NO:123), and CeresClone:758256 (SEQ ID NO:124). FIG. 1 and the other alignment figures provided herein were produced using MUSCLE version 3.52 based on the sequence alignments generated with ProbCon (Do et al., Genome Res., 15(2):330-40 (2005)) version 1.11.

FIGS. 2A-2B are an alignment of the amino acid sequence of Annot ID 837136 (SEQ ID NO:126) with homologous and/or orthologous amino acid sequences CeresAnnot:1491360 (SEQ ID NO:129), gi|50944321 (SEQ ID NO:130), and CeresClone:1784441 (SEQ ID NO:132).

FIGS. 3A-3C are an alignment of the amino acid sequence of Annot ID 860676 (SEQ ID NO:136) with homologous and/or orthologous amino acid sequences CeresClone:1948359 (SEQ ID NO:138), CeresAnnot:1472020 (SEQ ID NO:140), CeresClone:1924069 (SEQ ID NO:142), CeresClone:350091 (SEQ ID NO:143), CeresClone:1791482 (SEQ ID NO:145), gi|50912563 (SEQ ID NO:146), and CeresClone:917285 (SEQ ID NO:147).

FIGS. 4A-4C are an alignment of the amino acid sequence of Annot ID 860791 (SEQ ID NO:149) with homologous and/or orthologous amino acid sequences CeresClone:477792 (SEQ ID NO:153), CeresClone:677424 (SEQ ID NO:154), gi|51091033 (SEQ ID NO:155), CeresClone:336720 (SEQ ID NO:156), CeresClone:1790816 (SEQ ID NO:158), and Ceres Clone:1930079 (SEQ ID NO:319).

FIGS. 5A-5B are an alignment of the amino acid sequence of Locus At1g08200 (Ceres ANNOT ID no. 863641; SEQ ID NO:160) with homologous and/or orthologous amino acid sequences CeresClone:1459647 (SEQ ID NO:162), Ceres Annot ID:1541782 (SEQ ID NO:165), gi|85718018 (SEQ ID NO:168), gi|37379419 (SEQ ID NO:169), gi|34905954 (SEQ ID NO:171), and gi|92894433 (SEQ ED NO:172).

FIG. 6 is an alignment of the amino acid sequence of Annot ID 867623 (SEQ ID NO:176) with homologous and/or orthologous amino acid sequences CeresClone:873156 (SEQ ID NO:177), gi|83032230 (SEQ ID NO:178), CeresClone:1121732 (SEQ ID NO:180), and gi|92881787 (SEQ ID NO:181).

FIGS. 7A-7B are an alignment of the amino acid sequence of Annot ID 868753 (SEQ ID NO:183) with homologous and/or orthologous amino acid sequences CeresAnnot:1441800 (SEQ ID NO:185), CeresClone:1924705 (SEQ ID NO:187), and CeresClone:624590 (SEQ ID NO:188).

FIGS. 8A-8B are an alignment of the amino acid sequence of Annot ID 870466 (SEQ ID NO:196) with homologous and/or orthologous amino acid sequences gi|90657629 (SEQ ID NO:197), CeresClone:1883580 (SEQ ID NO:199), CeresAnnot:1450185 (SEQ ID NO:201), and gi|50916595 (SEQ ID NO:202).

FIGS. 9A-9B are an alignment of the amino acid sequence of Annot ID 887718 (SEQ ID NO:204) with homologous and/or orthologous amino acid sequences CeresClone:1835843 (SEQ ID NO:206), CeresAnnot:1457442 (SEQ ID NO:208), CeresClone:546224 (SEQ ID NO:211), gi|88604930 (SEQ ID NO:213), and gi|53653786 (SEQ ID NO:214).

FIG. 10 is an alignment of the amino acid sequence of CeresClone 1014844 (SEQ ID NO:218) with homologous and/or orthologous amino acid sequence gi|89257493 (SEQ ID NO:220).

FIGS. 11A-11B are an alignment of the amino acid sequence of CeresClone 11114 (SEQ ID NO:226) with homologous and/or orthologous amino acid sequences CeresClone:464185 (SEQ ID NO:227), gi|47717927 (SEQ ID NO:229), CeresAnnot:1498092 (SEQ ID NO:231), gi|92870641 (SEQ ID NO:234), CeresClone:1277160 (SEQ ID NO:235), gi|606942 (SEQ ID NO:236), gi|86438624 (SEQ ID NO:237), and gi|50947359 (SEQ ID NO:238).

FIGS. 12A-12E are an alignment of the amino acid sequence of CeresClone 114130 (SEQ ID NO:240) with homologous and/or orthologous amino acid sequences CeresClone:1920088 (SEQ ID NO:242), CeresAnnot:1448109 (SEQ ID NO:250), gi|82568711 (SEQ ID NO:257), gi|27475616 (SEQ ID NO:258), CeresClone:660782 (SEQ ID NO:259), gi|50926145 (SEQ ID NO:262), CeresClone:465877 (SEQ ID NO:263), gi|32400295 (SEQ ID NO:267), CeresClone:741711 (SEQ ID NO:268), CeresClone:1795778 (SEQ ID NO:270), gi|6469032 (SEQ ID NO:273), gi|40644084 (SEQ ID NO:274), gi|76573303 (SEQ ID NO:275), and gi|3288180 (SEQ ID NO:276).

FIG. 13 is an alignment of the amino acid sequence of CeresClone 38915 (SEQ ID NO:286) with homologous and/or orthologous amino acid sequence CeresClone:1375697 (SEQ ID NO:287).

FIGS. 14A-14F are an alignment of the amino acid sequence of CeresClone 8049 (SEQ ID NO:291) with homologous and/or orthologous amino acid sequences CeresClone:1365873 (SEQ ID NO:292), gi|1679853 (SEQ ID NO:293), gi|57639629 (SEQ ID NO:294), CeresClone:538586 (SEQ ID NO:296), gi|68271859 (SEQ ID NO:297), gi|7271916 (SEQ ID NO:300), gi|3023436 (SEQ ID NO:302), CeresAnnot:1514289 (SEQ ID NO:304), gi|684942 (SEQ ID NO:305), gi|1000519 (SEQ ID NO:306), gi|92873946 (SEQ ID NO:307), gi|992610 (SEQ ID NO:308), gi|47680455 (SEQ ID NO:309), gi|13249171 (SEQ ID NO:311), gi|48093469 (SEQ ID NO:312), gi|46394464 (SEQ ID NO:313), gi|24745969 (SEQ ID NO:314), gi|82941443 (SEQ ID NO:315), gi|40795556 (SEQ ID NO:316), gi|5739373 (SEQ ID NO:323), gi|55724835 (SEQ ID NO:324), gi|1934859 (SEQ ID NO:326), gi|6561881 (SEQ ID NO:327), CeresClone:1605906 (SEQ ID NO:329), gi|30580342 (SEQ ID NO:330), CeresClone:1756603 (SEQ ID NO:332), gi|2995934 (SEQ ID NO:333), CeresClone:700120 (SEQ ID NO:337), gi|96772920 (SEQ ID NO:338), gi|49618875 (SEQ ID NO:339), and gi|4104459 (SEQ ID NO:340).

FIGS. 15A-15G are an alignment of the amino acid sequence of Annot. ID 858797 (SEQ ID NO:134) with homologous and/or orthologous amino acid sequences gi|147744710 (SEQ ID NO:492), gi|89058600 (SEQ ID NO:494), gi|124430478 (SEQ ID NO:495), CeresClone 1836832 (SEQ ID NO:498), gi|83638483 (SEQ ID NO:503), Annot. ID 460633 (SEQ ID NO:505), Annot. ID 1471346 (SEQ ID NO:507), gi|119720796 (SEQ ID NO:508), gi|110931646 (SEQ ID NO:509), gi|92878899 (SEQ ID NO:514), gi|1841475 (SEQ ID NO:515), gi|39725415 (SEQ ID NO:516), gi|1167484 (SEQ ID NO:517), gi|126653935 (SEQ ID NO:518), gi|6552361 (SEQ ID NO:519), gi|126567773 (SEQ ID NO:521), gi|66736124 (SEQ ID NO:530), gi|145306631 (SEQ ID NO:531), gi|75107028 (SEQ ID NO:532), gi|127579 (SEQ ID NO:533), gi|38707418 (SEQ ID NO:534), gi|2605617 (SEQ ID NO:536), gi|38707432 (SEQ ID NO:538), gi|125487106 (SEQ ID NO:539), CeresClone 764797 (SEQ ID NO:542), CeresClone 1418548 (SEQ ID NO:544), gi|51872289 (SEQ ID NO:546), gi|119220854 (SEQ ID NO:547), gi|101919348 (SEQ ID NO:548), gi|125562458 (SEQ ID NO:549), gi|9072766 (SEQ ID NO:552), gi|76789657 (SEQ ID NO:560), gi|41581480 (SEQ ID NO:563), gi|148524147 (SEQ ID NO:564), gi|22266673 (SEQ ID NO:565), gi|19055 (SEQ ID NO:567), gi|23307803 (SEQ ID NO:568), gi|126567771 (SEQ ID NO:569), gi|28628961 (SEQ ID NO:570), gi|29824962 (SEQ ID NO:571), gi|42541177 (SEQ ID NO:572), and gi|148524145 (SEQ ID NO:574).

FIGS. 16A-16R are an alignment of the amino acid sequence of Annot ID 869790 (SEQ ID NO:190) with homologous and/or orthologous amino acid sequences gi|56605372 (SEQ ID NO:575), gi|33286376 (SEQ ID NO:576), gi|1170555 (SEQ ID NO:577), CeresClone 1838010 (SEQ ID NO:579), gi|231757 (SEQ ID NO:580), Annot ID 1521032 (SEQ ID NO:583), gi|7332271 (SEQ ID NO:586), CeresClone 9016 (SEQ ID NO:589), CeresClone 1086143 (SEQ ID NO:592), gi|114199044 (SEQ ID NO:595), gi|3913295 (SEQ ID NO:599), CeresClone 561287 (SEQ ID NO:601), gi|116908 (SEQ ID NO:602), gi|92878636 (SEQ ID NO:603), gi|1169009 (SEQ ID NO:604), gi|29839377 (SEQ ID NO:605), gi|12003964 (SEQ ID NO:606), gi|396589 (SEQ ID NO:608), gi|4104224 (SEQ ID NO:610), gi|29839259 (SEQ ID NO:613), gi|18033964 (SEQ ID NO:614), gi|77818928 (SEQ ID NO:616), CeresClone 1064285 (SEQ ID NO:621), gi|14578615 (SEQ ID NO:622), gi|7271883 (SEQ ID NO:626), gi|29839290 (SEQ ID NO:627), gi|38047397 (SEQ ID NO:628), gi|29839288 (SEQ ID NO:629), gi|29839289 (SEQ ID NO:630), gi|1582580 (SEQ ID NO:631), gi|57157826 (SEQ ID NO:632), gi|97974184 (SEQ ID NO:633), gi|567077 (SEQ ID NO:635), gi|24212067 (SEQ ID NO:636), gi|3913289 (SEQ ID NO:637), CeresClone 1869486 (SEQ ID NO:640), gi|29839421 (SEQ ID NO:641), gi|125560205 (SEQ ID NO:643), gi|125602246 (SEQ ID NO:644), gi|1669591 (SEQ ID NO:646), gi|22652500 (SEQ ID NO:647), gi|89113191 (SEQ ID NO:648), gi|68159362 (SEQ ID NO:650), gi|29839344 (SEQ ID NO:651), gi|4808524 (SEQ ID NO:652), gi|29839258 (SEQ ID NO:657), gi|109255537 (SEQ ID NO:658), gi|1314742 (SEQ ID NO:659), gi|7528266 (SEQ ID NO:660), gi|51980212 (SEQ ID NO:662), gi|74053618 (SEQ ID NO:663), and gi|47232556 (SEQ ID NO:664).

FIGS. 17A-17R are an alignment of the amino acid sequence of Annot ID 1365873 (SEQ ID NO:192) with gi|56605372 (SEQ ID NO:665), gi|4574324 (SEQ ID NO:666), gi|1777386 (SEQ ID NO:668), gi|24212392 (SEQ ID NO:669), gi|87887871 (SEQ ID NO:670), gi|33286376 (SEQ ID NO:671), gi|1170555 (SEQ ID NO:672), CeresClone 1847526 (SEQ ID NO:676), gi|231757 (SEQ ID NO:677), Annot ID 1521032 (SEQ ID NO:680), gi|7332271 (SEQ ID NO:683), gi|27808586 (SEQ ID NO:685), CeresClone 3828 (SEQ ID NO:687), CeresClone 1086143 (SEQ ID NO:689), gi|6760443 (SEQ ID NO:692), gi|114199044 (SEQ ID NO:693), gi|3913295 (SEQ ID NO:697), gi|116908 (SEQ ID NO:698), gi|92878636 (SEQ ID NO:699), gi|1169009 (SEQ ID NO:700), gi|29839377 (SEQ ID NO:701), gi|12003964 (SEQ ID NO:702), gi|396589 (SEQ ID NO:704), gi|5732000 (SEQ ID NO:706), gi|27531337 (SEQ ID NO:707), gi|2388664 (SEQ ID NO:708), gi|29839259 (SEQ ID NO:711), gi|18033964 (SEQ ID NO:712), gi|77818928 (SEQ ID NO:714), CeresClone 1453701 (SEQ ID NO:719), gi|14578615 (SEQ ID NO:720), gi|7271883 (SEQ ID NO:724), gi|29839290 (SEQ ID NO:725), gi|38047397 (SEQ ID NO:726), gi|29839288 (SEQ ID NO:727), gi|1582580 (SEQ ID NO:729), gi|57157826 (SEQ ID NO:730), gi|567077 (SEQ ID NO:733), CeresClone 1869486 (SEQ ID NO:739), gi|29839421 (SEQ ID NO:742), gi|125560205 (SEQ ID NO:744), gi|38565551 (SEQ ID NO:748), gi|22652500 (SEQ ID NO:749), gi|89113191 (SEQ ID NO:751), gi|29839344 (SEQ ID NO:754) gi|4808524 (SEQ ID NO:755), gi|29839258 (SEQ ID NO:760), gi|109255537 (SEQ ID NO:761), gi|7528266 (SEQ ID NO:762), gi|34398680 (SEQ ID NO:763), and gi|47232556 (SEQ ID NO:766).

FIGS. 18A-18E are an alignment of the amino acid sequence of Annot ID 1461478 (SEQ ID NO:342) with homologous and/or orthologous amino acid sequences gi|146217453 (SEQ ID NO:355), gi|34147924 (SEQ ID NO:356), Annot ID 1440199 (SEQ ID NO:358), gi|116831188 (SEQ ID NO:359), gi|71041096 (SEQ ID NO:363), gi|92891589 (SEQ ID NO:364), gi|39725413 (SEQ ID NO:365), gi|33320067 (SEQ ID NO:366), gi|1167486 (SEQ ID NO:367), gi|1002798 (SEQ ID NO:368), gi|547958 (SEQ ID NO:369), CeresClone 851672 (SEQ ID NO:371), CeresClone 1711992 (SEQ ID NO:373), gi|30024600 (SEQ ID NO:374), gi|11526775 (SEQ ID NO:375), gi|22795039 (SEQ ID NO:376), and gi|30575840 (SEQ ID NO:377).

FIGS. 19A-19V are an alignment of the amino acid sequence of Annot ID 1520476 (SEQ ID NO:344) with homologous and/or orthologous amino acid sequences gi|56605372 (SEQ ID NO:378), gi|4574324 (SEQ ID NO:379), gi|33286376 (SEQ ID NO:382), gi|133902324 (SEQ ID NO:383), gi|231757 (SEQ ID NO:388), Annot ID 1475680 (SEQ ID NO:390), gi|7332271 (SEQ ID NO:391), gi|15239571 (SEQ ID NO:393), CeresClone 1128033 (SEQ ID NO:397), gi|6760443 (SEQ ID NO:402), gi|3913295 (SEQ ID NO:407), CeresClone 535888 (SEQ ID NO:409), gi|116908 (SEQ ID NO:410), gi|92878636 (SEQ ID NO:411), gi|1169009 (SEQ ID NO:412), gi|29839377 (SEQ ID NO:413), gi|12003964 (SEQ ID NO:414), gi|396589 (SEQ ID NO:416), gi|5732000 (SEQ ID NO:418), gi|27531337 (SEQ ID NO:419), gi|2388664 (SEQ ID NO:420), gi|29839259 (SEQ ID NO:423), gi|28569609 (SEQ ID NO:424), gi|30385246 (SEQ ID NO:426), gi|729135 (SEQ ID NO:430), gi|33641726 (SEQ ID NO:436), gi|14578613 (SEQ ID NO:443), gi|133902310 (SEQ ID NO:447), gi|133902303 (SEQ ID NO:448), gi|7271883 (SEQ ID NO:449), gi|29839290 (SEQ ID NO:450), gi|38047397 (SEQ ID NO:451), gi|29839288 (SEQ ID NO:452), gi|1582580 (SEQ ID NO:454), gi|97974173 (SEQ ID NO:456), gi|24212064 (SEQ ID NO:458), gi|6688808 (SEQ ID NO:461), gi|3913289 (SEQ ID NO:462), CeresClone 1917412 (SEQ ID NO:465), gi|29839421 (SEQ ID NO:466), gi|125560205 (SEQ ID NO:468), gi|115474869 (SEQ ID NO:469), gi|1669591 (SEQ ID NO:471), gi|38565551 (SEQ ID NO:472), gi|29839361 (SEQ ID NO:474), gi|45444737 (SEQ ID NO:475), gi|29839344 (SEQ ID NO:477), gi|4808530 (SEQ ID NO:478), gi|109255537 (SEQ ID NO:484), gi|148337324 (SEQ ID NO:485), gi|7528266 (SEQ ID NO:486), and gi|145695037 (SEQ ID NO:488).

FIGS. 20A-20D are an alignment of the amino acid sequence of CeresClone 11988 (SEQ ID NO:281) with homologous and/or orthologous amino acid sequences Annot ID 1467144 (SEQ ID NO:770), gi|92867830 (SEQ ED NO:771), gi|7414433 (SEQ ID NO:772), gi|11071974 (SEQ ID NO:773), gi|419789 (SEQ ID NO:774), gi|33321023 (SEQ ID NO:775), gi|33321014 (SEQ ID NO:776), CeresClone 1145901 (SEQ ID NO:778), CeresClone 1876038 (SEQ ID NO:780), gi|125531206 (SEQ ID NO:781), and gi|22655795 (SEQ ID NO:783).

FIGS. 21A-21I are an alignment of the amino acid sequence of CeresClone 21243 (SEQ ID NO:284) with homologous and/or orthologous amino acid sequences CeresClone 1848247 (SEQ ID NO:788), gi|20466640 (SEQ ID NO:789), gi|31322578 (SEQ ID NO:790), gi|63252923 (SEQ ID NO:792), CeresClone 467981 (SEQ ID NO:794), gi|87241197 (SEQ ID NO:795), gi|57233056 (SEQ ID NO:796), gi|52353036 (SEQ ID NO:797), gi|21105748 (SEQ ID NO:798), gi|6730938 (SEQ ID NO:799), gi|58013003 (SEQ ID NO:800), gi|66275774 (SEQ ID NO:801), gi|115336267 (SEQ ID NO:804), gi|117586720 (SEQ ID NO:805), gi|73759951 (SEQ ID NO:806), gi|115336269 (SEQ ID NO:807), CeresClone 1824711 (SEQ ID NO:809), gi|82400207 (SEQ ID NO:810), gi|154362215 (SEQ ID NO:813), gi|78499704 (SEQ ID NO:814), and gi|82568708 (SEQ ID NO:815).

FIG. 22 is an alignment of the amino acid sequence of CeresClone 41046 (SEQ ID NO:289) with homologous and/or orthologous amino acid sequences gi|54634694 (SEQ ID NO:816) and gi|38322956 (SEQ ID NO:820).

DETAILED DESCRIPTION

The invention features methods and materials related to modulating (e.g., decreasing) the lignin content in plants. The methods can include transforming a plant cell with a nucleic acid encoding a lignin-modulating polypeptide, wherein expression of the polypeptide results in a modulated (e.g., increased or decreased) lignin content. Plant cells produced using such methods can be grown to produce plants having a modulated lignin content. Such plants can have a modulated amount and/or rate of lignin biosynthesis. For example, the rate of biosynthesis of one or more lignin monomers, e.g., monolignols, can be modulated. In some cases, the rate of polymerization of lignin monomers into lignin can be modulated. In addition, the structure and/or composition of lignin produced by transgenic plants described herein can vary from that produced by corresponding wild-type plants.

Polypeptides

The term “polypeptide” as used herein refers to a compound of two or more subunit amino acids, amino acid analogs, or other peptidomimetics, regardless of post-translational modification, e.g., phosphorylation or glycosylation. The subunits may be linked by peptide bonds or other bonds such as, for example, ester or ether bonds. The term “amino acid” refers to natural and/or unnatural or synthetic amino acids, including D/L optical isomers. Full-length proteins, analogs, mutants, and fragments thereof are encompassed by this definition.

Polypeptides described herein include lignin-modulating polypeptides. A lignin-modulating polypeptide typically is effective for modulating lignin content when expressed in a plant or plant cell. Modulation of the lignin content can be an increase or decrease in the amount and/or rate of biosynthesis of lignin relative to the corresponding amount and/or rate in a control plant. The structure of lignin, its composition (e.g., proportion of p-hydroxyphenyl (H), guaiacyl (G), or syringyl (S) units), or both can also be modulated. In some cases, the rate of polymerization of lignin monomers (e.g., p-coumaryl, coniferyl, and sinapyl alcohols) into lignin is modulated.

A lignin-modulating polypeptide can have an NAD epimerase/dehydratase domain characteristic of a nicotinamide adenine dinucleotide (NAD)-dependent epimerase/dehydratase polypeptide. The NAD-dependent epimerase/dehydratase family of proteins utilize NAD as a cofactor and use nucleotide-sugar substrates for a variety of chemical reactions. SEQ ID NO:149 and SEQ ID NO:160 set forth the amino acid sequences of DNA clones, identified herein as Ceres ANNOT ID no. 860791 (SEQ ID NO:148) and Ceres ANNOT ID no. 863641 (SEQ ID NO:159), respectively, each of which is predicted to encode a polypeptide containing an NAD_binding_(—)4 domain.

A lignin-modulating polypeptide can comprise the amino acid sequence set forth in SEQ ID NO:149 or SEQ ID NO:160. In some cases, a lignin-modulating polypeptide can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:149 or SEQ ID NO:160. For example, a lignin-modulating polypeptide can have an amino acid sequence with at least 30% sequence identity, e.g., 31%, 35%, 40%, 45%, 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%, sequence identity, to the amino acid sequence set forth in SEQ ID NO:149 or SEQ ID NO:160.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:149 and SEQ ID NO:160 are provided in FIGS. 4A-4C and FIGS. 5A-5B, respectively. For example, the alignment in FIGS. 4A-4C provides the amino acid sequences of Annot ID 860791 (SEQ ID NO:149), CeresClone:477792 (SEQ ID NO:153), CeresClone:677424 (SEQ ID NO:154), gi|51091033 (SEQ ID NO:155), CeresClone:336720 (SEQ ID NO:156), CeresClone:1790816 (SEQ ID NO:158), and Ceres Clone:1930079 (SEQ ID NO:319). Other homologs and/or orthologs of SEQ ID NO:149 include Public GI no. 15226135 (SEQ ID NO:150) and CeresClone 1930079 (SEQ ID NO:152).

The alignment in FIGS. 5A-5B provides the amino acid sequences of Locus At1g08200 (Ceres ANNOT ID no. 863641; SEQ ID NO:160), CeresClone:1459647 (SEQ ID NO:162), CeresGdna:1541782 (SEQ ID NO:165), gi|85718018 (SEQ ID NO:168), gi|37379419 (SEQ ID NO:169), gi|34905954 (SEQ ID NO:171), and gi|92894433 (SEQ ID NO:172). Other homologs and/or orthologs of SEQ ID NO:160 include Public GI no. 14596185 (SEQ ID NO:161), Public GI no. 60547725 (SEQ ID NO:163), Ceres ANNOT ID no. 1460446 (SEQ ID NO:167), Ceres CLONE ID no. 300029 (SEQ ID NO:170), Public GI no. 42602317 (SEQ ID NO:173), and Ceres CLONE ID no. 243057 (SEQ ID NO:174).

In some cases, a lignin-modulating polypeptide can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NO:150, SEQ ID NOs:152-156, SEQ ID NO:158, SEQ ID NOs:161-163, SEQ ID NO:165, SEQ ID NOs:167-174, and SEQ ID NO:319.

A lignin-modulating polypeptide can have a XET_C domain and a Glyco_hydro_(—)16 domain. The XET_C domain is characteristic of the C-terminus (about 60 amino acid residues) of a plant xyloglucan endo-transglycosylase (XET) polypeptide. Xyloglucan is the predominant hemicellulose in the cell walls of most dicotyledons. Xyloglucan forms a network with cellulose that strengthens the cell wall. XET catalyzes the splitting of xyloglucan chains and the linking of the newly generated reducing end to the non-reducing end of another xyloglucan chain, thereby loosening the cell wall. Polypeptides belonging to the XET_C polypeptide family also contain the Glyco_hydro_(—)16 domain characteristic of glycosyl hydrolase family 16 polypeptides. O-glycosyl hydrolases (EC 3.2.1.-) hydrolyze the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families. Since the folds of the polypeptides are better conserved than the sequences, some of the families can be grouped in “clans.” Glycoside hydrolase family 16 comprises enzymes with a number of known activities, including lichenase, xyloglucan xyloglucosyltransferase, agarase, kappa-carrageenase, endo-beta-1,3-glucanase, endo-beta-1,3-1,4-glucanase, and endo-beta-galactosidase. SEQ ID NO:204 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres ANNOT ID no. 887718 (SEQ ID NO:203), that is predicted to encode a polypeptide containing a XET_C domain and a Glyco_hydro_(—)16 domain.

A lignin-modulating polypeptide can comprise the amino acid sequence set forth in SEQ ID NO:204. In some cases, a lignin-modulating polypeptide can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:204. For example, a lignin-modulating polypeptide can have an amino acid sequence with at least 65% sequence identity, e.g., 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:204.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:204 are provided in FIGS. 9A-9B. For example, the alignment in FIGS. 9A-9B provides the amino acid sequences of Annot ID 887718 (SEQ ID NO:204), CeresClone:1835843 (SEQ ID NO:206), CeresAnnot:1457442 (SEQ ID NO:208), CeresClone:546224 (SEQ ID NO:211), gi|88604930 (SEQ ID NO:213), and gi|53653786 (SEQ ID NO:214). Other homologs and/or orthologs of SEQ ID NO:204 include Ceres CLONE ID no. 1836342 (SEQ ID NO:210), and Ceres CLONE ID no. 142634 (SEQ ID NO:212).

In some cases, a lignin-modulating polypeptide can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NO:206, SEQ ID NO:208, SEQ ID NOs:210-214.

A lignin-modulating polypeptide can have a Glyco_hydro_(—)9 domain characteristic of a glycosyl hydrolase family 9 polypeptide. Glycoside hydrolase family 9 comprises enzymes with several known activities, including endoglucanase and cellobiohydrolase. Glycosyl hydrolase family 9 was formerly known as cellulase family E. SEQ ID NO:136 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres ANNOT ID no. 860676 (SEQ ID NO:135), that is predicted to encode a polypeptide containing a Glyco_hydro_(—)9 domain.

In some cases, a lignin modulating polypeptide can have a Glyco_hydro_(—)17 domain characteristic of a glycosyl hydrolase family 17 polypeptide. Glycoside hydrolase family 17 comprises enzymes with several known activities, including endo-1,3-beta-glucosidase, lichenase, and exo-1,3-glucanase. These enzymes have been found in plants and fungi. SEQ ID NO:281 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 11988 (SEQ ID NO:280), that is predicted to encode a polypeptide containing a Glyco_hydro_(—)17 domain.

A lignin-modulating polypeptide can comprise the amino acid sequence set forth in SEQ ID NO:136 or SEQ ID NO:281. In some cases, a lignin-modulating polypeptide can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:136 or SEQ ID NO:281. For example, a lignin-modulating polypeptide can have an amino acid sequence with at least 60% sequence identity, e.g., 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:136 or SEQ ID NO:281.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:136 are provided in FIGS. 3A-3C. For example, the alignment in FIGS. 3A-3C provides the amino acid sequences of Annot ID 860676 (SEQ ID NO:136), CeresClone:1948359 (SEQ ID NO:138), CeresAnnot:1472020 (SEQ ID NO:140), CeresClone:1924069 (SEQ ID NO:142), CeresClone:350091 (SEQ ID NO:143), CeresClone:1791482 (SEQ ID NO:145), gi|50912563 (SEQ ID NO:146), and CeresClone:917285 (SEQ ID NO:147).

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:281 are provided in FIGS. 20A-20D. For example, the alignment in FIGS. 20A-20D provides the amino acid sequences of CeresClone 11988 (SEQ ID NO:281), Annot ID 1467144 (SEQ ID NO:770), gi|92867830 (SEQ ID NO:771), gi|7414433 (SEQ ID NO:772), gi|11071974 (SEQ ID NO:773), gi|419789 (SEQ ID NO:774), gi|33321023 (SEQ ID NO:775), gi|33321014 (SEQ ID NO:776), CeresClone 1145901 (SEQ ID NO:778), CeresClone 1876038 (SEQ ID NO:780), gi|125531206 (SEQ ID NO:781), and gi|22655795 (SEQ ID NO:783). Other homologs and/or orthologs of SEQ ID NO:281 include Annot ID 1441963 (SEQ ID NO:768), gi|125561574 (SEQ ID NO:782) gi|115481224 (SEQ ID NO:784), gi|115451885 (SEQ ID NO:785), and gi|125585592 (SEQ ID NO:786).

In some cases, a lignin-modulating polypeptide can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NO:138, SEQ ID NO:140, SEQ ID NOs:142-143, SEQ ID NOs:145-147, SEQ ID NO:768, SEQ ID NOs:770-776, SEQ ID NO:778, or SEQ ID NOs:780-786.

A lignin-modulating polypeptide can have a Dimerisation domain and a Methyltransf_(—)2 domain characteristic of O-methyltransferase polypeptides. The Dimerisation domain is found at the N-terminus of a variety of plant O-methyltransferase polypeptides and has been shown to mediate dimerization of these polypeptides. O-methyltransferase polypeptides transfer methyl groups, e.g., from S-adenosyl methionine, to nitrogen, oxygen, or carbon atoms. For example, O-methyltransferases modify DNA, RNA, polypeptides, and small molecules such as catechol for regulatory purposes. In prokaryotes, the major role of DNA methylation is to protect host DNA against degradation by restriction enzymes. In eukaryotes, DNA methylation has been implicated in the control of several cellular processes, including differentiation, gene regulation, and embryonic development. O-methyltransferases have a common catalytic domain structure, which may be universal among S-adenosyl methionine-dependent methyltransferases. SEQ ID NO:190, SEQ ID NO:192, and SEQ ID NO:344 set forth the amino acid sequences of DNA clones, identified herein as Ceres ANNOT ID no. 869790 (SEQ ID NO:189), Ceres ANNOT ID no. 869854 (SEQ ID NO:191), and Ceres LOCUS ID no. 1520476 (SEQ ID NO:343), respectively, each of which is predicted to encode a polypeptide containing a Dimerisation domain and a Methyltransf_(—)2 domain.

In some cases, a lignin-modulating polypeptide can have a Methyltransf_(—)3 domain characteristic of O-methyltransferase polypeptides. The Methyltransf_(—)3 family includes catechol O-methyltransferase, caffeoyl-CoA O-methyltransferase, and a family of bacterial O-methyltransferases that may be involved in antibiotic production. SEQ ID NO:291 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 8049 (SEQ ID NO:290), that is predicted to encode a polypeptide containing a Methyltransf_(—)3 domain.

A lignin-modulating polypeptide can comprise the amino acid sequence set forth in SEQ ID NO:190, SEQ ID NO:192, SEQ ID NO:344, or SEQ ID NO:291. In some cases, a lignin-modulating polypeptide can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:190, SEQ ID NO:192, SEQ ID NO:344, or SEQ ID NO:291. For example, a lignin-modulating polypeptide can have an amino acid sequence with at least 30% sequence identity, e.g., 31%, 35%, 40%, 45%, 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%, sequence identity, to the amino acid sequence set forth in SEQ ID NO:190, SEQ ID NO:192, SEQ ID NO:344, or SEQ ID NO:291.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:190 are provided in FIGS. 16A-16R. For example, the alignment in FIGS. 16A-16R provides the amino acid sequences of Annot ID 869790 (SEQ ID NO:190), gi|56605372 (SEQ ID NO:575), gi|33286376 (SEQ ID NO:576), gi|1170555 (SEQ ID NO:577), CeresClone 1838010 (SEQ ID NO:579), gi|231757 (SEQ ID NO:580), Annot ID 1521032 (SEQ ID NO:583), gi|7332271 (SEQ ID NO:586), CeresClone 9016 (SEQ ID NO:589), CeresClone 1086143 (SEQ ID NO:592), gi|114199044 (SEQ ID NO:595), gi|3913295 (SEQ ID NO:599), CeresClone 561287 (SEQ ID NO:601), gi|116908 (SEQ ID NO:602), gi|92878636 (SEQ ID NO:603), gi|1169009 (SEQ ID NO:604), gi|29839377 (SEQ ID NO:605), gi|12003964 (SEQ ID NO:606), gi|396589 (SEQ ID NO:608), gi|4104224 (SEQ ID NO:610), gi|29839259 (SEQ ID NO:613), gi|18033964 (SEQ ID NO:614), gi|77818928 (SEQ ID NO:616), CeresClone 1064285 (SEQ ID NO:621), gi|14578615 (SEQ ID NO:622), gi|7271883 (SEQ ID NO:626), gi|29839290 (SEQ ID NO:627), gi|38047397 (SEQ ID NO:628), gi|29839288 (SEQ ID NO:629), gi|29839289 (SEQ ID NO:630), gi|1582580 (SEQ ID NO:631), gi|57157826 (SEQ ID NO:632), gi|97974184 (SEQ ID NO:633), gi|567077 (SEQ ID NO:635), gi|24212067 (SEQ ID NO:636), gi|3913289 (SEQ ID NO:637), CeresClone 1869486 (SEQ ID NO:640), gi|29839421 (SEQ ID NO:641), gi|125560205 (SEQ ID NO:643), gi|125602246 (SEQ ID NO:644), gi|1669591 (SEQ ID NO:646), gi|22652500 (SEQ ID NO:647), gi|89113191 (SEQ ID NO:648), gi|68159362 (SEQ ID NO:650), gi|29839344 (SEQ ID NO:651), gi|4808524 (SEQ ID NO:652), gi|29839258 (SEQ ID NO:657), gi|109255537 (SEQ ID NO:658), gi|1314742 (SEQ ID NO:659), gi|7528266 (SEQ ID NO:660), gi|51980212 (SEQ ID NO:662), gi|74053618 (SEQ ID NO:663), and gi|47232556 (SEQ ID NO:664).

Other homologs and/or orthologs of SEQ ID NO:190 include gi|29839286 (SEQ ID NO:581), Annot ID 1472909 (SEQ ID NO:585), gi|444327 (SEQ ID NO:587), gi|21617938 (SEQ ID NO:590), CeresClone 1118817 (SEQ ID NO:594), gi|114199048 (SEQ ID NO:596), gi|114199046 (SEQ ID NO:597), gi|114199050 (SEQ ID NO:598), gi|30315948 (SEQ ID NO:607), gi|396591 (SEQ ID NO:609), gi|2388664 (SEQ ID NO:611), gi|4104220 (SEQ ID NO:612), gi|28569609 (SEQ ID NO:615), gi|30385246 (SEQ ID NO:617), gi|570057 (SEQ ID NO:619), gi|14578611 (SEQ ID NO:623), gi|14578613 (SEQ ID NO:624), gi|14578617 (SEQ ID NO:625), gi|97974173 (SEQ ID NO:634), gi|38502831 (SEQ ID NO:638), gi|29839420 (SEQ ID NO:642), gi|115474869 (SEQ ID NO:645), gi|89113193 (SEQ ID NO:649), gi|4808526 (SEQ ID NO:653), gi|4808530 (SEQ ID NO:654), gi|4808528 (SEQ ID NO:655), gi|4808522 (SEQ ID NO:656), and gi|34398680 (SEQ ID NO:661).

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:192 are provided in FIGS. 17A-17R. For example, the alignment in FIGS. 17A-17R provides the amino acid sequences of Annot ID 1365873 (SEQ ID NO:192), gi|56605372 (SEQ ID NO:665), gi|4574324 (SEQ ID NO:666), gi|1777386 (SEQ ID NO:668), gi|24212392 (SEQ ID NO:669), gi|87887871 (SEQ ID NO:670), gi|33286376 (SEQ ID NO:671), gi|1170555 (SEQ ID NO:672), CeresClone 1847526 (SEQ ID NO:676), gi|231757 (SEQ ID NO:677), Annot ID 1521032 (SEQ ID NO:680), gi|7332271 (SEQ ID NO:683), gi|27808586 (SEQ ID NO:685), CeresClone 3828 (SEQ ID NO:687), CeresClone 1086143 (SEQ ID NO:689), gi|6760443 (SEQ ID NO:692), gi|114199044 (SEQ ID NO:693), gi|3913295 (SEQ ID NO:697), gi|116908 (SEQ ID NO:698), gi|92878636 (SEQ ID NO:699), gi|1169009 (SEQ ID NO:700), gi|29839377 (SEQ ID NO:701), gi|12003964 (SEQ ID NO:702), gi|396589 (SEQ ID NO:704), gi|5732000 (SEQ ID NO:706), gi|27531337 (SEQ ID NO:707), gi|2388664 (SEQ ID NO:708), gi|29839259 (SEQ ID NO:711), gi|18033964 (SEQ ID NO:712), gi|77818928 (SEQ ID NO:714), CeresClone 1453701 (SEQ ID NO:719), gi|14578615 (SEQ ID NO:720), gi|7271883 (SEQ ID NO:724), gi|29839290 (SEQ ID NO:725), gi|38047397 (SEQ ID NO:726), gi|29839288 (SEQ ID NO:727), gi|1582580 (SEQ ID NO:729), gi|57157826 (SEQ ID NO:730), gi|567077 (SEQ ID NO:733), CeresClone 1869486 (SEQ ID NO:739), gi|29839421 (SEQ ID NO:742), gi|125560205 (SEQ ID NO:744), gi|38565551 (SEQ ID NO:748), gi|22652500 (SEQ ID NO:749), gi|89113191 (SEQ ID NO:751), gi|29839344 (SEQ ID NO:754) gi|4808524 (SEQ ID NO:755), gi|29839258 (SEQ ID NO:760), gi|109255537 (SEQ ID NO:761), gi|7528266 (SEQ ID NO:762), gi|34398680 (SEQ ID NO:763), and gi|47232556 (SEQ ID NO:766).

Other homologs and/or orthologs of SEQ ID NO:192 include gi|1568664 (SEQ ID NO:667), CeresClone 1838010 (SEQ ID NO:674), gi|29839286 (SEQ ID NO:678), Annot ID 1472909 (SEQ ID NO:682), gi|444327 (SEQ ID NO:684), CeresClone 118817 (SEQ ID NO:691), gi|114199046 (SEQ ID NO:694), gi|114199048 (SEQ ID NO:695), gi|114199050 (SEQ ID NO:696), gi|30315948 (SEQ ID NO:703), gi|396591 (SEQ ID NO:705), gi|4104224 (SEQ ID NO:709), gi|4104220 (SEQ ID NO:710), gi|28569609 (SEQ ID NO:713), CeresClone 570057 (SEQ ID NO:716), gi|30385246 (SEQ ID NO:717), gi|14578613 (SEQ ID NO:721), gi|14578611 (SEQ ID NO:722), gi|14578617 (SEQ ID NO:723), gi|29839289 (SEQ ID NO:728), gi|97974184 (SEQ ID NO:731), gi|97974173 (SEQ ID NO:732), gi|24212064 (SEQ ID NO:734), gi|24212067 (SEQ ID NO:735), gi|3913289 (SEQ ID NO:736), gi|38502831 (SEQ ID NO:737), CeresClone 1770156 (SEQ ID NO:741), gi|29839420 (SEQ ID NO:743), gi|115474869 (SEQ ID NO:745), gi|125602246 (SEQ ID NO:746), gi|1669591 (SEQ ID NO:747), gi|29839361 (SEQ ID NO:750), gi|89113193 (SEQ ID NO:752), gi|68159362 (SEQ ID NO:753), gi|4808528 (SEQ ID NO:756), gi|4808522 (SEQ ID NO:757), gi|4808526 (SEQ ID NO:758), gi|4808530 (SEQ ID NO:759), gi|51980212 (SEQ ID NO:764), and gi|74053618 (SEQ ID NO:765).

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:344 are provided in FIGS. 19A-19V. For example, the alignment in FIGS. 19A-19V provides the amino acid sequences of Annot ID 1520476 (SEQ ID NO:344), gi|56605372 (SEQ ID NO:378), gi|4574324 (SEQ ID NO:379), gi|33286376 (SEQ ID NO:382), gi|133902324 (SEQ ID NO:383), gi|231757 (SEQ ID NO:388), Annot ID 1475680 (SEQ ID NO:390), gi|7332271 (SEQ ID NO:391), gi|15239571 (SEQ ID NO:393), CeresClone 1128033 (SEQ ID NO:397), gi|6760443 (SEQ ID NO:402), gi|3913295 (SEQ ID NO:407), CeresClone 535888 (SEQ ID NO:409), gi|116908 (SEQ ID NO:410), gi|92878636 (SEQ ID NO:411), gi|1169009 (SEQ ID NO:412), gi|29839377 (SEQ ID NO:413), gi|12003964 (SEQ ID NO:414), gi|396589 (SEQ ID NO:416), gi|5732000 (SEQ ID NO:418), gi|27531337 (SEQ ID NO:419), gi|2388664 (SEQ ID NO:420), gi|29839259 (SEQ ID NO:423), gi|28569609 (SEQ ID NO:424), gi|30385246 (SEQ ID NO:426), gi|729135 (SEQ ID NO:430), gi|33641726 (SEQ ID NO:436), gi|14578613 (SEQ ID NO:443), gi|133902310 (SEQ ID NO:447), gi|133902303 (SEQ ID NO:448), gi|7271883 (SEQ ID NO:449), gi|29839290 (SEQ ID NO:450), gi|38047397 (SEQ ID NO:451), gi|29839288 (SEQ ID NO:452), gi|1582580 (SEQ ID NO:454), gi|97974173 (SEQ ID NO:456), gi|24212064 (SEQ ID NO:458), gi|6688808 (SEQ ID NO:461), gi|3913289 (SEQ ID NO:462), CeresClone 1917412 (SEQ ID NO:465), gi|29839421 (SEQ ID NO:466), gi|125560205 (SEQ ID NO:468), gi|115474869 (SEQ ID NO:469), gi|1669591 (SEQ ID NO:471), gi|38565551 (SEQ ID NO:472), gi|29839361 (SEQ ID NO:474), gi|45444737 (SEQ ID NO:475), gi|29839344 (SEQ ID NO:477), gi|4808530 (SEQ ID NO:478), gi|109255537 (SEQ ID NO:484), gi|148337324 (SEQ ID NO:485), gi|7528266 (SEQ ID NO:486), and gi|145695037 (SEQ ID NO:488).

Other homologs and/or orthologs of SEQ ID NO:344 include gi|1568664 (SEQ ID NO:380), gi|24212392 (SEQ ID NO:381), gi|133902316 (SEQ ID NO:384), gi|133902317 (SEQ ID NO:385), CeresClone 1930109 (SEQ ID NO:387), gi|444327 (SEQ ID NO:392), gi|2781394 (SEQ ID NO:394), gi|15223364 (SEQ ID NO:395), CeresClone 1118817 (SEQ ID NO:399), CeresClone 1091294 (SEQ ID NO:401), gi|114199048 (SEQ ID NO:403), gi|114199044 (SEQ ID NO:404), gi|114199046 (SEQ ID NO:405), gi|114199050 (SEQ ID NO:406), gi|30315948 (SEQ ID NO:415), gi|396591 (SEQ ID NO:417), gi|4104220 (SEQ ID NO:421), gi|4104224 (SEQ ID NO:422), gi|18033964 (SEQ ID NO:425), gi|77818928 (SEQ ID NO:427), gi|145693798 (SEQ ID NO:428), gi|145693796 (SEQ ID NO:429), gi|33641710 (SEQ ID NO:431), gi|33641704 (SEQ ID NO:432), gi|33641706 (SEQ ID NO:433), gi|33641708 (SEQ ID NO:434), gi|33641718 (SEQ ID NO:435), gi|33641752 (SEQ ID NO:437), gi|33641714 (SEQ ID NO:438), gi|33641732 (SEQ ID NO:439), gi|33641716 (SEQ ID NO:440), gi|33641720 (SEQ ID NO:441), gi|33641740 (SEQ ID NO:442), gi|14578611 (SEQ ID NO:444), gi|14578615 (SEQ ID NO:445), gi|14578617 (SEQ ID NO:446), gi|29839289 (SEQ ID NO:453), gi|57157826 (SEQ ID NO:455), gi|97974184 (SEQ ID NO:457), gi|24212067 (SEQ ID NO:459), gi|567077 (SEQ ID NO:460), gi|38502831 (SEQ ID NO:463), gi|29839420 (SEQ ID NO:467), gi|125602246 (SEQ ID NO:470), gi|22652500 (SEQ ID NO:473), gi|68159362 (SEQ ID NO:476), gi|4808524 (SEQ ID NO:479), gi|4808522 (SEQ ID NO:480), gi|4808528 (SEQ ID NO:481), gi|4808526 (SEQ ID NO:482), gi|29839258 (SEQ ID NO:483), gi|34398680 (SEQ ID NO:487), gi|51980212 (SEQ ID NO:489), gi|74053618 (SEQ ID NO:490), and gi|32440933 (SEQ ID NO:491).

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:291 are provided in FIGS. 14A-14F. For example, the alignment in FIGS. 14A-14F provides the amino acid sequences of CeresClone 8049 (SEQ ID NO:291), CeresClone:1365873 (SEQ ID NO:292), gi|1679853 (SEQ ID NO:293), gi|57639629 (SEQ ID NO:294), CeresClone:538586 (SEQ ID NO:296), gi|68271859 (SEQ ID NO:297), gi|7271916 (SEQ ID NO:300), gi|3023436 (SEQ ID NO:302), CeresAnnot:1514289 (SEQ ID NO:304), gi|684942 (SEQ ID NO:305), gi|1000519 (SEQ ID NO:306), gi|92873946 (SEQ ID NO:307), gi|992610 (SEQ ID NO:308), gi|47680455 (SEQ ID NO:309), gi|13249171 (SEQ ID NO:311), gi|48093469 (SEQ ID NO:312), gi|46394464 (SEQ ID NO:313), gi|24745969 (SEQ ID NO:314), gi|82941443 (SEQ ID NO:315), gi|40795556 (SEQ ID NO:316), gi|5739373 (SEQ ID NO:323), gi|55724835 (SEQ ID NO:324), gi|1934859 (SEQ ID NO:326), gi|6561881 (SEQ ID NO:327), CeresClone:1605906 (SEQ ID NO:329), gi|30580342 (SEQ ID NO:330), CeresClone:1756603 (SEQ ID NO:332), gi|2995934 (SEQ ID NO:333), CeresClone:700120 (SEQ ID NO:337), gi|96772920 (SEQ ID NO:338), gi|49618875 (SEQ ID NO:339), and gi|4104459 (SEQ ID NO:340).

Other homologs and/or orthologs of SEQ ID NO:291 include Public GI no. 2511737 (SEQ ID NO:295), Ceres CLONE ID no. 541352 (SEQ ID NO:298), Public GI no. 1574946 (SEQ ID NO:317), Public GI no. 1103487 (SEQ ID NO:318), Public GI no. 1575436 (SEQ ID NO:319), Ceres ANNOT ID no. 1441117 (SEQ ID NO:321), Public GI no. 1575440 (SEQ ID NO:322), Public GI no. 1622926 (SEQ ID NO:325), Public GI no. 3319278 (SEQ ID NO:328), Public GI no. 5101868 (SEQ ID NO:334), Ceres CLONE ID no. 353929 (SEQ ID NO:335), and Ceres CLONE ID no. 464460 (SEQ ID NO:336).

In some cases, a lignin-modulating polypeptide can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:292-298, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NOs:304-309, SEQ ID NOs:311-319, SEQ ID NOs:321-330, SEQ ID NOs:332-340, SEQ ID NOs:378-385, SEQ ID NOs:387-388, SEQ ID NO:390-395, SEQ ID NOs:397-399, SEQ ID NOs:401-407, SEQ ID NOs:409-463, SEQ ID NOs:465-491, SEQ ID NOs:575-577, SEQ ID NOs:579-581, SEQ ID NO:583, SEQ ID NOs:585-587, SEQ ID NOs:589-590, SEQ ID NO:592, SEQ ID NOs:594-599, SEQ ID NOs:601-617, SEQ ID NO:619, SEQ ID NOs:621-638, SEQ ID NOs:640-672, SEQ ID NO:674, SEQ ID NOs:676-678, SEQ ID NO:680, SEQ ID NOs:682-685, SEQ ID NOs:687, SEQ ID NO:689, SEQ ID NOs:691-714, SEQ ID NOs:716-717, SEQ ID NOs:719-737, SEQ ID NO:739, SEQ ID NOs:742-758, or SEQ ID NOs:760-766.

A lignin-modulating polypeptide can contain a Transferase domain characteristic of transferase enzymes. Members of the transferase family of polypeptides include anthranilate N-hydroxycinnamoyl/benzoyltransferase, which catalyzes the first committed reaction of phytoalexin biosynthesis. Another member of the family, deacetylvindoline 4-O-acetyltransferase (EC:2.3.1.107), catalyzes the last step in vindoline biosynthesis. The family also includes trichothecene 3-O-acetyltransferase. SEQ ID NO:240 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 114130 (SEQ ID NO:239), that is predicted to encode a polypeptide containing a Transferase domain.

A lignin-modulating polypeptide can comprise the amino acid sequence set forth in SEQ ID NO:240. In some cases, a lignin-modulating polypeptide can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:240. For example, a lignin-modulating polypeptide can have an amino acid sequence with at least 45% sequence identity, e.g., 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:240.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth SEQ ID NO:240 are provided in FIGS. 12A-12E. For example, the alignment in FIGS. 12A-12E provides the amino acid sequences of CeresClone 114130 (SEQ ID NO:240), CeresClone:1920088 (SEQ ID NO:242), CeresAnnot:1448109 (SEQ ID NO:250), gi|82568711 (SEQ ID NO:257), gi|27475616 (SEQ ID NO:258), CeresClone:660782 (SEQ ID NO:259), gi|50926145 (SEQ ID NO:262), CeresClone:465877 (SEQ ID NO:263), gi|32400295 (SEQ ID NO:267), CeresClone:741711 (SEQ ID NO:268), CeresClone:1795778 (SEQ ID NO:270), gi|6469032 (SEQ ID NO:273), gi|40644084 (SEQ ID NO:274), gi|76573303 (SEQ ID NO:275), and gi|3288180 (SEQ ID NO:276). Other homologs and/or orthologs of SEQ ID NO:240 include Ceres CLONE ID no. 1920450 (SEQ ID NO:244), Ceres CLONE ID no. 1941995 (SEQ ID NO:246), Ceres CLONE ID no. 1920870 (SEQ ID NO:248), Ceres ANNOT ID no. 1501106 (SEQ ID NO:252), Ceres ANNOT ID no. 1483635 (SEQ ID NO:254), Ceres ANNOT ID no. 1537107 (SEQ ID NO:256), Ceres CLONE ID no. 1620792 (SEQ ID NO:260), Ceres CLONE ID no. 566887 (SEQ ID NO:261), Public GI no. 50910387 (SEQ ID NO:264), Ceres CLONE ID no. 1598714 (SEQ ID NO:265), Ceres CLONE ID no. 1691303 (SEQ ID NO:266), Public GI no. 32400291 (SEQ ID NO:271), Public GI no. 32400293 (SEQ ID NO:272), Public GI no. 2239091 (SEQ ID NO:277), Public GI no. 2239087 (SEQ ID NO:278), and Public GI no. 2239085 (SEQ ID NO:279).

In some cases, a lignin-modulating polypeptide can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NO:242, SEQ ID NO:244, SEQ ID NO:246, SEQ ID NO:248, SEQ ID NO:250, SEQ ID NO:252, SEQ ID NO:254, SEQ ID NOs:256-268, and SEQ ID NOs:270-279.

A lignin-modulating polypeptide can contain an Exostosin domain characteristic of the Exostosin (EXT) family of polypeptides. The EXT1 and EXT2 polypeptides are glycosyltransferases having both D-glucuronyl (GlcA) and N-acetyl-D-glucosaminoglycan (GIcNAC) transferase activities. These polypeptides are involved in the chain elongation step of heparan sulphate biosynthesis. SEQ ID NO:183 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres ANNOT ID no. 868753 (SEQ ID NO:182), that is predicted to encode a polypeptide containing an Exostosin domain.

A lignin-modulating polypeptide can comprise the amino acid sequence set forth in SEQ ID NO:183. In some cases, a lignin-modulating polypeptide can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:183. For example, a lignin-modulating polypeptide can have an amino acid sequence with at least 55% sequence identity, e.g., 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:183.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:183 are provided in FIGS. 7A-7B. For example, the alignment in FIGS. 7A-7B provides the amino acid sequences of Annot ID 868753 (SEQ ID NO:183), CeresAnnot:1441800 (SEQ ID NO:185), CeresClone:1924705 (SEQ ID NO:187), and CeresClone:624590 (SEQ ID NO:188).

In some cases, a lignin-modulating polypeptide can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NO:185, and SEQ ID NOs:187-188.

A lignin-modulating polypeptide can contain a Pollen_allerg_(—)1 domain and a DPBB_(—)1 domain (Rare lipoprotein A (RlpA)-like double-psi beta-barrel fold). A Pollen_allerg_(—)1 domain is characteristic of Lolium perenne (perennial rye grass) pollen allergens Lol PI, PII and PIII. A DPBB_(—)1 domain is found in the N-terminus of pollen allergens as well as in some bacterial and eukaryotic lipoproteins, such as RlpA. The DPBB fold is often an enzymatic domain. Pollen allergens share a high degree of sequence similarity with expansins. Expansins are polypeptides that mediate cell wall extension in plants. Expansin polypeptides are believed to act as a chemical grease, allowing polymers to slide past one another by disrupting non-covalent hydrogen bonds that hold many wall polymers to one another. This process is not degradative and does not weaken the wall, which could otherwise rupture under internal pressure during growth. Sequence comparisons indicate at least four distinct expansin cDNAs in rice and at least six in Arabidopsis. The polypeptides are highly conserved in size and sequence (75-95% amino acid sequence similarity). It is thought that several highly-conserved tryptophans may function in expansin binding to cellulose, or other glycans. SEQ ID NO:222 and SEQ ID NO:286 set forth the amino acid sequences of DNA clones, identified herein as Ceres CLONE ID no. 108362 (SEQ ID NO:221) and Ceres CLONE ID no. 38915 (SEQ ID NO:285), respectively, each of which is predicted to encode a polypeptide containing a Pollen_allerg_(—)1 domain and a DPBB_(—)1 domain.

A lignin-modulating polypeptide can comprise the amino acid sequence set forth in SEQ ID NO:222 or SEQ ID NO:286. In some cases, a lignin-modulating polypeptide can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:222 or SEQ ID NO:286. For example, a lignin-modulating polypeptide can have an amino acid sequence with at least 75% sequence identity, e.g., 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:222 or SEQ ID NO:286.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:286 are provided in FIG. 13. For example, the alignment in FIG. 13 provides the amino acid sequences of CeresClone 38915 (SEQ ID NO:286) and CeresClone:1375697 (SEQ ID NO:287).

In some cases, a lignin-modulating polypeptide can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to SEQ ID NO:287.

A lignin-modulating polypeptide can contain a p450 domain characteristic of a cytochrome P450 polypeptide. The cytochrome P450 enzymes constitute a superfamily of haem-thiolate proteins. P450 enzymes usually act as terminal oxidases in multicomponent electron transfer chains, called P450-containing monooxygenase systems, and are involved in metabolism of a plethora of both exogenous and endogenous compounds. The conserved core is composed of a coil referred to as the “meander,” a four-helix bundle, helices J and K, and two sets of beta-sheets. These regions constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the fifth ligand for the haem iron), the proton-transfer groove, and the absolutely conserved EXXR motif in helix K. SEQ ID NO:96, SEQ ID NO:98, and SEQ ID NO:289 set forth the amino acid sequences of DNA clones, identified herein as Ceres ANNOT ID no. 521911 (SEQ ID NO:95), Ceres ANNOT ID no. 535161 (SEQ ID NO:97), and Ceres CLONE ID no. 41046 (SEQ ID NO:288), respectively, each of which is predicted to encode a polypeptide containing a p450 domain.

A lignin-modulating polypeptide can comprise the amino acid sequence set forth in SEQ ID NO:96, SEQ ID NO:98, or SEQ ID NO:289. In some cases, a lignin-modulating polypeptide can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:96, SEQ ID NO:98, or SEQ ID NO:289. For example, a lignin-modulating polypeptide can have an amino acid sequence with at least 55% sequence identity, e.g., 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:96, SEQ ID NO:98, or SEQ ID NO:289.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:98 are provided in FIGS. 1A-1F. For example, the alignment in FIGS. 1A-1F provides the amino acid sequences of Annot ID 535161 (SEQ ID NO:98), gi|10197650 (SEQ ID NO:101), gi|47933890 (SEQ ID NO:105), gi|85001689 (SEQ ID NO:106), gi|5731998 (SEQ ID NO:107), CeresAnnot:1487764 (SEQ ID NO:109), gi|77744233 (SEQ ID NO:110), gi|46403211 (SEQ ID NO:117), gi|92888952 (SEQ ID NO:118), gi|57470997 (SEQ ID NO:119), gi|5002354 (SEQ ID NO:120), CeresClone:1585325 (SEQ ID NO:121), gi|110289397 (SEQ ID NO:123), and CeresClone:758256 (SEQ ID NO:124). Other homologs and/or orthologs of SEQ ID NO:98 include Public GI no. 12578895 (SEQ ID NO:99), Public GI no. 12578911 (SEQ ID NO:100), Public GI no. 10197652 (SEQ ID NO:102), Public GI no. 10197654 (SEQ ID NO:103), Public GI no. 110432088 (SEQ ID NO:104), Ceres CLONE ID no. 1636607 (SEQ ID NO:111), Public GI no. 6688937 (SEQ ID NO:113), Public GI no. 77744235 (SEQ ID NO:114), Ceres ANNOT ID no. 1457344 (SEQ ID NO:116), and Ceres CLONE ID no. 1600886 (SEQ ID NO:122).

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:289 are provided in FIG. 22. For example, the alignment in FIG. 1 provides the amino acid sequences of CeresClone 41046 (SEQ ID NO:289), gi|54634694 (SEQ ID NO:816), and gi|38322956 (SEQ ID NO:820).

In some cases, a lignin-modulating polypeptide can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:99-107, SEQ ID NOs:109-111, SEQ ID NOs:113-114, SEQ ID NOs:116-124, SEQ ID NO:816, or SEQ ID NO:820.

A lignin-modulating polypeptide can have a phytochelatin synthetase-like conserved region (Phytochel_synth domain) characteristic of a family of plant polypeptides believed to be phytochelatin synthetases. Phytochelatin synthetase (EC 2.3.2.15) is a dipeptidyltranspeptidase enzyme responsible for the production of phytochelatins, small glutamic acid, cysteine and glycine-rich peptides. Phytochelatin synthetase catalyzes the synthesis of phytochelatins by transferring a γ-Glu-Cys moiety of glutatlhione to glutathione or to other phytochelatins. SEQ ID NO:196 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres ANNOT ID no. 870466 (SEQ ID NO:195), that is predicted to encode a polypeptide containing a Phytochel_synth domain.

A lignin-modulating polypeptide can comprise the amino acid sequence set forth in SEQ ID NO:196. In some cases, a lignin-modulating polypeptide can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:196. For example, a lignin-modulating polypeptide can have an amino acid sequence with at least 60% sequence identity, e.g., 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:196.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:196 are provided in FIGS. 8A-8B. For example, the alignment in FIGS. 8A-8B provides the amino acid sequences of Annot ID 870466 (SEQ ID NO:196), gi|90657629 (SEQ ID NO:197), CeresClone:1883580 (SEQ ID NO:199), CeresAnnot:1450185 (SEQ ID NO:201), and gi|50916595 (SEQ ID NO:202).

In some cases, a lignini-modulating polypeptide can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NO:197, SEQ ID NO:199, and SEQ ID NOs:201-202.

A lignin-modulating polypeptide can contain a Fasciclin domain. The FAS1 or BIgH3 domain is an extracellular module of about 140 amino acid residues. It has been suggested that the FAS1 domain represents an ancient cell adhesion domain common to plants and animals. Related FAS1 domains are also found in bacteria. Most FAS1 domain-containing polypeptides are GPI anchored and contain two or four copies of the domain. FAS1 domains of the BIgH3 polypeptide mediate cell adhesion through an interaction with alpha3/beta1 integrin. A short motif (EPDIM), located on the C-terminal side of the fourth domain, is essential for binding to integrin. The crystal structure of two FAS1 domains (FAS1 3-4) of a fas1 polypeptide have been solved. Each domain comprises a seven-stranded wedge and at least five alpha helices. Two well-ordered N-acetylglucosamine moieties attached to a conserved asparagine are located in the interface region between the two FAS1 domains. The Arabidopsis fasciclin-like arabinogalactan polypeptides are examples of FAS1 domain-containing polypeptides. SEQ ID NO:226 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 11114 (SEQ ID NO:225), that is predicted to encode a polypeptide containing a Fasciclin domain.

A lignin-modulating polypeptide can comprise the amino acid sequence set forth SEQ ID NO:226. In some cases, a lignin-modulating polypeptide can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:226. For example, a lignin-modulating polypeptide can have an amino acid sequence with at least 45% sequence identity, e.g., 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:226.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:226 are provided in FIGS. 11A-11B. For example, the alignment in FIGS. 11A-11B provides the amino acid sequences of CeresCione 11114 (SEQ ID NO:226), CeresClone:464185 (SEQ ID NO:227), gi|47717927 (SEQ ID NO:229), CeresAnnot:1498092 (SEQ ID NO:231), gi|92870641 (SEQ ID NO:234), CeresClone:1277160 (SEQ ID NO:235), gi|606942 (SEQ ID NO:236), gi|86438624 (SEQ ID NO:237), and gi|50947359 (SEQ ID NO:238). Other homologs and/or orthologs of SEQ ID NO:226 include Ceres ANNOT ID no. 1472093 (SEQ ID NO:233).

In some cases, a lignin-modulating polypeptide can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NO:227, SEQ ID NO:229, SEQ ID NO:231, or SEQ ID NOs:233-238.

A lignin-modulating polypeptide can contain a myb-like DNA binding domain characteristic of myb-like transcription factor polypeptides. The retroviral oncogene v-myb and its cellular counterpart c-myb encode nuclear DNA binding polypeptides. These polypeptides belong to the SANT domain family that specifically recognize the sequence YAAC(G/T)G. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA binding. Arabidopsis thaliana is estimated to contain more than 140 MYB or MYB-related genes. In contrast to animals, plants contain a MYB-protein subfamily that is characterized by the R2R3-type MYB domain. Classical MYB factors, which are related to c-MYB, seem to be involved in the control of the cell cycle in animals, plants and other higher eukaryotes. R2R3-type MYB genes control many aspects of plant secondary metabolism, as well as the identity and fate of plant cells. SEQ ID NO:134, SEQ ID NO:216, and SEQ ID NO:342 set forth the amino acid sequences of DNA clones, identified herein as Ceres ANNOT ID no. 858797 (SEQ ID NO:133), Ceres CLONE ID no. 1006105 (SEQ ID NO:215), and Ceres LOCUS ID no. 1461478 (SEQ ID NO:341), respectively, each of which is predicted to encode a polypeptide containing a myb-like DNA binding domain.

A lignin-modulating polypeptide can comprise the amino acid sequence set forth in SEQ ID NO:134, SEQ ID NO:216, or SEQ ID NO:342. In some cases, a lignin-modulating polypeptide can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:134, SEQ ID NO:216, or SEQ ID NO:342. For example, a lignin-modulating polypeptide can have an amino acid sequence with at least 40% sequence identity, e.g., 45%, 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:134, SEQ ID NO:216, or SEQ ID NO:342.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:134 and SEQ ID NO:342 are provided in FIGS. 15A-15G and FIGS. 18A-18E, respectively. For example, the alignment in FIGS. 15A-15G provides the amino acid sequences of Annot. ID 858797 (SEQ ID NO:134), gi|147744710 (SEQ ID NO:492), gi|89058600 (SEQ ID NO:494), gi|124430478 (SEQ ID NO:495), CeresClone 1836832 (SEQ ID NO:498), gi|83638483 (SEQ ID NO:503), Annot. ID 460633 (SEQ ID NO:505), Annot. ID 1471346 (SEQ ID NO:507), gi|119720796 (SEQ ID NO:508), gi|110931646 (SEQ ID NO:509), gi|92878899 (SEQ ID NO:514), gi|1841475 (SEQ ID NO:515), gi|39725415 (SEQ ID NO:516), gi|1167484 (SEQ ID NO:517), gi|126653935 (SEQ ID NO:518), gi|6552361 (SEQ ID NO:519), gi|126567773 (SEQ ID NO:521), gi|66736124 (SEQ ID NO:530), gi|145306631 (SEQ ID NO:531), gi|75107028 (SEQ ID NO:532), gi|127579 (SEQ ID NO:533), gi|38707418 (SEQ ID NO:534), gi|2605617 (SEQ ID NO:536), gi|38707432 (SEQ ID NO:538), gi|125487106 (SEQ ID NO:539), CeresClone 764797 (SEQ ID NO:542), CeresClone 1418548 (SEQ ID NO:544), gi|51872289 (SEQ ID NO:546), gi|119220854 (SEQ ID NO:547), gi|101919348 (SEQ ID NO:548), gi|125562458 (SEQ ID NO:549), gi|19072766 (SEQ ID NO:552), gi|76789657 (SEQ ID NO:560), gi|41581480 (SEQ ID NO:563), gi|148524147 (SEQ ID NO:564), gi|22266673 (SEQ ID NO:565), gi|19055 (SEQ ID NO:567), gi|23307803 (SEQ ID NO:568), gi|126567771 (SEQ ID NO:569), gi|28628961 (SEQ ID NO:570), gi|29824962 (SEQ ID NO:571), gi|42541177 (SEQ ID NO:572), and gi|148524145 (SEQ ID NO:574).

Other homologs and/or orthologs of SEQ ID NO:134 include gi|147744720 (SEQ ID NO:493), gi|13346194 (SEQ ID NO:496), gi|23476279 (SEQ ID NO:499), gi|437327 (SEQ ID NO:500), gi|1976145 (SEQ ID NO:502), gi|114384137 (SEQ ID NO:510), gi|10931806 (SEQ ID NO:511), CeresClone 1642529 (SEQ ID NO:513), gi|1732247 (SEQ ID NO:520), gi|126567788 (SEQ ID NO:522), gi|126567775 (SEQ ID NO:523), gi|7673088 (SEQ ID NO:524), gi|126567782 (SEQ ID NO:525), gi|126567786 (SEQ ID NO:526), gi|126567784 (SEQ ID NO:527), gi|7673086 (SEQ ID NO:528), gi|61696099 (SEQ ID NO:529), gi|38707422 (SEQ ID NO:535), gi|2605619 (SEQ ID NO:537), gi|47680445 (SEQ ID NO:540), gi|89143143 (SEQ ID NO:545), gi|125562456 (SEQ ID NO:550), gi|125533629 (SEQ ID NO:551), gi|115477685 (SEQ ID NO:553), gi|115484469 (SEQ ID NO:554), gi|125594329 (SEQ ID NO:555), gi|55733916 (SEQ ID NO:556), gi|125576429 (SEQ ID NO:557), gi|115441355 (SEQ ID NO:558), gi|77553801 (SEQ ID NO:559), gi|89258177 (SEQ ID NO:561), gi|89258179 (SEQ ID NO:562), gi|22266675 (SEQ ID NO:566), and gi|42541167 (SEQ ID NO:573).

The alignment in FIGS. 18A-18E provides the amino acid sequences of Annot ID 1461478 (SEQ ID NO:342), gi|146217453 (SEQ ID NO:355), gi|34147924 (SEQ ID NO:356), Annot ID 1440199 (SEQ ID NO:358), gi|116831188 (SEQ ID NO:359), gi|71041096 (SEQ ID NO:363), gi|92891589 (SEQ ID NO:364), gi|39725413 (SEQ ID NO:365), gi|33320067 (SEQ ID NO:366), gi|1167486 (SEQ ID NO:367), gi|1002798 (SEQ ID NO:368), gi|547958 (SEQ ID NO:369), CeresClone 851672 (SEQ ID NO:371), CeresClone 1711992 (SEQ ID NO:373), gi|30024600 (SEQ ID NO:374), gi|11526775 (SEQ ID NO:375), gi|22795039 (SEQ ID NO:376), and gi|30575840 (SEQ ID NO:377). Other homologs and/or orthologs of SEQ ID NO:342 include gi|15231922 (SEQ ID NO:360), gi|51970238 (SEQ ID NO:361), and gi|45357090 (SEQ ID NO:362).

In some cases, a lignin-modulating polypeptide can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NO:342, SEQ ID NOs:355-356, SEQ ID NOs:358-369, SEQ ID NO:371, SEQ ID NOs:373-377, SEQ ID NOs:492-496, SEQ ID NOs:498-500, SEQ ID NOs:502-503, SEQ ID NO:505, SEQ ID NOs:507-511, SEQ ID NOs:513-540, or SEQ ID NOs:544-574.

A lignin-modulating polypeptide can have a NAM domain characteristic of a No apical meristem (NAM) polypeptide. No apical meristem (NAM) polypeptides are plant development polypeptides. NAM is indicated as having a role in determining positions of meristems and primordia. The NAC domain (NAM for Petunia hybrida and ATAF1, ATAF2, and CUC2 for Arabidopsis) is an N-terminal module of about 160 amino acids, which is found in polypeptides of the NAC family of plant-specific transcriptional regulators (no apical meristem polypeptides). NAC proteins are involved in developmental processes, including formation of the shoot apical meristem, floral organs and lateral shoots, as well as in plant hormonal control and defense. The NAC domain is accompanied by diverse C-terminal transcriptional activation domains. The NAC domain has been shown to be a DNA-binding domain and a dimerization domain. SEQ ID NO:284 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 21243 (SEQ ID NO:283), which is predicted to encode a polypeptide containing a NAM domain.

A lignin-modulating polypeptide can comprise the amino acid sequence set forth in SEQ ID NO:284. In some cases, a lignin-modulating polypeptide can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:284. For example, a lignin-modulating polypeptide can have an amino acid sequence with at least 40% sequence identity, e.g., 45%, 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:284.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:284 are provided in FIGS. 21A-21I. For example, the alignment in FIGS. 21A-21I provides the amino acid sequences of CeresClone 21243 (SEQ ID NO:284), CeresClone 1848247 (SEQ ID NO:788), gi|20466640 (SEQ ID NO:789), gi|31322578 (SEQ ID NO:790), gi|63252923 (SEQ ID NO:792), CeresClone 467981 (SEQ ID NO:794), gi|87241197 (SEQ ID NO:795), gi|57233056 (SEQ ID NO:796), gi|52353036 (SEQ ID NO:797), gi|21105748 (SEQ ID NO:798), gi|6730938 (SEQ ID NO:799), gi|58013003 (SEQ ID NO:800), gi|66275774 (SEQ ID NO:801), gi|15336267 (SEQ ID NO:804), gi|117586720 (SEQ ID NO:805), gi|73759951 (SEQ ID NO:806), gi|115336269 (SEQ ID NO:807), CeresClone 1824711 (SEQ ID NO:809), gi|82400207 (SEQ ID NO:810), gi|154362215 (SEQ ID NO:813), gi|78499704 (SEQ ID NO:814), and gi|82568708 (SEQ ID NO:815). Other homologs and/or orthologs of SEQ ID NO:284 include gi|31322576 (SEQ ID NO:791), gi|66275772 (SEQ ID NO:802), gi|51702424 (SEQ ID NO:803), gi|82400213 (SEQ ID NO:811), and gi|82400209 (SEQ ID NO:812).

In some cases, a lignin-modulating polypeptide can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:788-792, SEQ ID NOs:794-807, and SEQ ID NOs:809-815.

A lignin-modulating polypeptide can have one or more domains characteristic of a homeobox polypeptide. For example, a lignin-modulating polypeptide can contain a homeobox domain, a HALZ domain, and an HD-ZIP_N domain. The homeobox domain is involved in DNA binding through a helix-turn-helix (HTH) structure. The HTH motif is characterized by two alpha-helices, which make intimate contacts with DNA and are joined by a short turn. Examples of homeodomain-containing polypeptides include transcriptional regulators encoded by hox genes that operate differential genetic programs along the anterior-posterior axis of animal bodies. The homeobox associated leucine zipper (HALZ) domain is a plant specific leucine zipper that is associated with a homeobox. The HD-ZIP_N domain is characteristic of the N-termini of plant homeobox-leucine zipper polypeptides. Homeodomain leucine zipper (HDZip) genes encode putative transcription factors that are unique to plants. This observation suggests that homeobox-leucine zipper genes evolved after the divergence of plants and animals, perhaps to mediate specific regulatory events. SEQ ID NO:218 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 1014844 (SEQ ID NO:217), which is predicted to encode a polypeptide having a homeobox domain, a HALZ domain, and an HD-ZIP_N domain.

A lignin-modulating polypeptide can comprise the amino acid sequence set forth in SEQ ID NO:218. In some cases, a lignin-modulating polypeptide can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:218. For example, a lignin-modulating polypeptide can have an amino acid sequence with at least 80% sequence identity, e.g., 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:218.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth SEQ ID NO:218 are provided in FIG. 10. For example, the alignment in FIG. 10 provides the amino acid sequences of CeresClone 1014844 (SEQ ID NO:218) and gi|89257493 (SEQ ID NO:220). Other homologs and/or orthologs of SEQ ID NO:218 include Ceres CLONE ID no. 26013 (SEQ ID NO:219).

In some cases, a lignin-modulating polypeptide can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:219-220.

SEQ ID NO:176 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres ANNOT ID no. 867623 (SEQ ID NO:175), which is predicted to encode a polypeptide that does not have homology to an existing polypeptide family based on Pfam analysis. A lignin-modulating polypeptide can comprise the amino acid sequence set forth in SEQ ID NO:176. In some cases, a lignin-modulating polypeptide can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:176. For example, a lignin-modulating polypeptide can have an amino acid sequence with at least 45% sequence identity, e.g., 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:176.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth SEQ ID NO:176 are provided in FIG. 6. For example, the alignment in FIG. 6 provides the amino acid sequences of Annot ID 867623 (SEQ ID NO:176), CeresClone:873156 (SEQ ID NO:177), gi|83032230 (SEQ ID NO:178), CeresClone:1121732 (SEQ ID NO:180), and gi|92881787 (SEQ ID NO:181). Other homologs and/or orthologs of SEQ ID NO:176 include Ceres CLONE ID no. 971850 (SEQ ID NO:179).

In some cases, a lignin-modulating polypeptide can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:177-181.

SEQ ID NO:126 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres ANNOT ID no. 837136 (SEQ ID NO:125), that is predicted to encode a polypeptide that does not have homology to an existing polypeptide family based on Pfam analysis. A lignin-modulating polypeptide can comprise the amino acid sequence set forth in SEQ ID NO:126. In some cases, a lignin-modulating polypeptide can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:126. For example, a regulatory polypeptide can have an amino acid sequence with at least 50% sequence identity, e.g., 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:126.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:126 are provided in FIGS. 2A-2B. For example, the alignment in FIGS. 2A-2B provides the amino acid sequences of Annot ID 837136 (SEQ ID NO:126), CeresAnnot:1491360 (SEQ ID NO:129), gi|50944321 (SEQ ID NO:130), and CeresClone:1784441 (SEQ ID NO:132). Other homologs and/or orthologs of SEQ ID NO:126 include Public GI no. 12323467 (SEQ ID NO:127).

In some cases, a lignin-modulating polypeptide can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NO:127, SEQ ID NOs:129-130, or SEQ ID NO:132.

A lignin-modulating polypeptide encoded by a recombinant nucleic acid can be a native lignin-modulating polypeptide, i.e., one or more additional copies of the coding sequence for a lignin-modulating polypeptide that is naturally present in the cell. Alternatively, a lignin-modulating polypeptide can be heterologous to the cell, e.g., a transgenic Populus plant can contain the coding sequence for an enzyme from an Arabidopsis plant.

A lignin-modulating polypeptide can include additional amino acids that are not involved in modulating gene expression, and thus can be longer than would otherwise be the case. For example, a lignin-modulating polypeptide can include an amino acid sequence that functions as a reporter. Such a lignin-modulating polypeptide can be a fusion protein in which a green fluorescent protein (GFP) polypeptide is fused to, e.g., SEQ ID NO:96, or in which a yellow fluorescent protein (YFP) polypeptide is fused to, e.g., SEQ ID NO:98. In some embodiments, a lignin-modulating polypeptide includes a purification tag, a chloroplast transit peptide, a mitochondrial transit peptide, an amyloplast peptide, or a leader sequence added to the amino or carboxyl terminus.

In some embodiments, one or more functional homologs of a reference lignin-modulating polypeptide defined by one or more of the pfam descriptions indicated above are suitable for use as lignin-modulating polypeptides. A functional homolog is a polypeptide that has sequence similarity to a reference polypeptide, and that carries out one or more of the biochemical or physiological function(s) of the reference polypeptide. A functional homolog and the reference polypeptide may be natural occurring polypeptides, and the sequence similarity may be due to convergent or divergent evolutionary events. As such, functional homologs are sometimes designated in the literature as homologs, or orthologs, or paralogs. Variants of a naturally occurring functional homolog, such as polypeptides encoded by mutants of a wild type coding sequence, may themselves be functional homologs. Functional homologs can also be created via site-directed mutagenesis of the coding sequence for a lignin-modulating polypeptide, or by combining domains from the coding sequences for different naturally-occurring lignin-modulating polypeptides (“domain swapping”). The term “functional homolog” is sometimes applied to the nucleic acid that encodes a functionally homologous polypeptide.

Lignin-modulating polypeptide candidates suitable for use in the invention can be identified by analysis of nucleotide and polypeptide sequence alignments. For example, performing a query on a database of nucleotide or polypeptide sequences can identify homologs and/or orthologs of lignin-modulating polypeptides. Sequence analysis can involve BLAST, Reciprocal BLAST, or PSI-BLAST analysis of nonredundant databases using known lignin-modulating polypeptide amino acid sequences. Those polypeptides in the database that have greater than 40% sequence identity can be identified as candidates for further evaluation for suitability as lignin-modulating polypeptides. Amino acid sequence similarity allows for conservative amino acid substitutions, such as substitution of one hydrophobic residue for another or substitution of one polar residue for another. If desired, manual inspection of such candidates can be carried out in order to narrow the number of candidates to be further evaluated. Manual inspection can be performed by selecting those candidates that appear to have domains suspected of being present in lignin-modulating polypeptides, e.g., conserved functional domains.

The identification of conserved regions in a template or subject polypeptide can facilitate production of variants of lignin-modulating polypeptides. Conserved regions can be identified by locating a region within the primary amino acid sequence of a template polypeptide that is a repeated sequence, forms some secondary structure (e.g., helices and beta sheets), establishes positively or negatively charged domains, or represents a protein motif or domain. See, e.g., the Pfam web site describing consensus sequences for a variety of protein motifs and domains at sanger.ac.uk/Pfam and genome.wustl.edu/Pfam. A description of the information included at the Pfam database is described in Sonnhammer et al., Nucl. Acids Res., 26:320-322 (1998); Sonnhammer et al., Proteins, 28:405-420 (1997); and Bateman et al., Nucl. Acids Res., 27:260-262 (1999). Amino acid residues corresponding to Pfam domains included in lignin-modulating polypeptides provided herein are set forth in the sequence listing. For example, amino acid residues 30 to 89 of the amino acid sequence set forth in SEQ ID NO:190 correspond to a dimerisation domain, as indicated in fields <222> and <223> for SEQ ID NO:190 in the sequence listing.

Conserved regions also can be determined by aligning sequences of the same or related polypeptides from closely related species. Closely related species preferably are from the same family. In some embodiments, alignment of sequences from two different species is adequate. For example, sequences from Arabidopsis thaliana and Glycine max can be used to identify one or more conserved regions.

Typically, polypeptides that exhibit at least about 40% amino acid sequence identity are useful to identify conserved regions. Conserved regions of related polypeptides can exhibit at least 45% amino acid sequence identity, e.g., at least 50%, at least 60%, at least 70%, at least 80%, or at least 90% amino acid sequence identity. In some embodiments, a conserved region of target and template polypeptides exhibit at least 92%, 94%, 96%, 98%, or 99% amino acid sequence identity. Amino acid sequence identity can be deduced from amino acid or nucleotide sequences. In certain cases, highly conserved domains have been identified within lignin-modulating polypeptides. These conserved regions can be useful in identifying functionally similar (orthologus) lignin-modulating polypeptides.

In some instances, suitable lignin-modulating polypeptides can be synthesized on the basis of functional domains and/or conserved regions in polypeptides that are homologous lignin-modulating polypeptides. Domains are groups of substantially contiguous amino acids in a polypeptide that can be used to characterize protein families and/or parts of proteins. Such domains have a “fingerprint” or “signature” that can comprise conserved (1) primary sequence, (2) secondary structure, and/or (3) three-dimensional conformation. Generally, domains are correlated with specific in vitro and/or in vivo activities. A domain can have a length of from 10 amino acids to 400 amino acids, e.g., 10 to 50 amino acids, or 25 to 100 amino acids, or 35 to 65 amino acids, or 35 to 55 amino acids, or 45 to 60 amino acids, or 200 to 300 amino acids, or 300 to 400 amino acids.

Representative homologs and/or orthologs of lignin-modulating polypeptides are shown in FIGS. 1-22. Each Figure represents an alignment of the amino acid sequence of a lignin-modulating polypeptide with the amino acid sequences of corresponding homologs and/or orthologs. Amino acid sequences of lignin-modulating polypeptides and their corresponding homologs and/or orthologs have been aligned to identify conserved amino acids as shown in FIGS. 1-22. A dash in an aligned sequence represents a gap, i.e., a lack of an amino acid at that position. Identical amino acids or conserved amino acid substitutions among aligned sequences are identified by boxes.

The identification of conserved regions in a lignin-modulating polypeptide facilitates production of variants of lignin-modulating polypeptides. Variants of lignin-modulating polypeptides typically have 10 or fewer conservative amino acid substitutions within the primary amino acid sequence, e.g., 7 or fewer conservative amino acid substitutions, 5 or fewer conservative amino acid substitutions, or between 1 and 5 conservative substitutions. Useful variant polypeptides can be constructed based on the conserved regions in FIG. 1, FIG. 2, FIG. 3, FIG. 4, FIG. 5, FIG. 6, FIG. 7, FIG. 8, FIG. 9, FIG. 10, FIG. 11, FIG. 12, FIG. 13, FIG. 14, FIG. 15, FIG. 16, FIG. 17, FIG. 18, FIG. 19, FIG. 20, FIG. 21, or FIG. 22. Such a polypeptide includes the conserved regions arranged in the order depicted in a Figure from amino-terminal end to carboxy-terminal end. Such a polypeptide may also include zero, one, or more than one amino acid in positions marked by dashes. When no amino acids are present at positions marked by dashes, the length of such a polypeptide is the sum of the amino acid residues in all conserved regions. When amino acids are present at all positions marked by dashes, such a polypeptide has a length that is the sum of the amino acid residues in all conserved regions and all dashes.

A conserved domain in certain cases may be a localization domain, an activation domain, a repression domain, an oligomerization domain, a catalytic domain, or a DNA binding domain. Consensus domains and conserved regions can be identified by homologous polypeptide sequence analysis as described above. The suitability of polypeptides for use as lignin-modulating polypeptides can be evaluated by functional complementation studies.

A lignin-modulating polypeptide also can be a fragment of a naturally occurring lignin-modulating polypeptide. In certain cases, such as transcription factor lignin-modulating polypeptides, a fragment can comprise the DNA-binding and transcription-regulating domains of the naturally occurring lignin-modulating polypeptide. In some cases, such as enzyme lignin-modulating polypeptides, a fragment can comprise the catalytic domain of the naturally occurring lignin-modulating polypeptide.

Useful lignin-modulating polypeptides also can include those that fit a Hidden Markov Model based on the polypeptides set forth in any one of FIGS. 1-22. A Hidden Markov Model (HMM) is a statistical model of a consensus sequence for a group of functional homologs. See, Durbin et al., Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Cambridge University Press, Cambridge, UK (1998). An HMM is generated by the program HMMER 2.3.2 with default program parameters, using the sequences of the group of functional homologs as input. The multiple sequence alignment is generated by ProbCons (Do et al., Genome Res., 15(2):330-40 (2005)) version 1.11 using a set of default parameters: —c, —consistency REPS of 2; —ir, —iterative-refinement REPS of 100; —pre, —pre-training REPS of 0. ProbCons is a public domain software program provided by Stanford University.

The default parameters for building an HMM (hmmbuild) are as follows: the default “architecture prior” (archpri) used by MAP architecture construction is 0.85, and the default cutoff threshold (idlevel) used to determine the effective sequence number is 0.62. HMMER 2.3.2 was released Oct. 3, 2003 under a GNU general public license, and is available from various sources on the World Wide Web such as hmmer.janelia.org; hmmer.wustl.edu; and fr.com/hmmer232/. Hmmbuild outputs the model as a text file.

The HMM for a group of functional homologs can be used to determine the likelihood that a candidate lignin-modulating polypeptide sequence is a better fit to that particular HMM than to a null HMM generated using a group of sequences that are not structurally or functionally related. The likelihood that a candidate polypeptide sequence is a better fit to an HMM than to a null HMM is indicated by the HMM bit score, a number generated when the candidate sequence is fitted to the HMM profile using the HMMER hmmsearch program. The following default parameters are used when running hmmsearch: the default E-value cutoff (E) is 10.0, the default bit score cutoff (T) is negative infinity, the default number of sequences in a database (Z) is the real number of sequences in the database, the default E-value cutoff for the per-domain ranked hit list (domE) is infinity, and the default bit score cutoff for the per-domain ranked hit list (domT) is negative infinity. A high HMM bit score indicates a greater likelihood that the candidate sequence carries out one or more of the biochemical or physiological function(s) of the polypeptides used to generate the HMM. A high HMM bit score is at least 20, and often is higher. Slight variations in the HMM bit score of a particular sequence can occur due to factors such as the order in which sequences are processed for alignment by multiple sequence alignment algorithms such as the ProbCons program. Nevertheless, such HMM bit score variation is minor.

The lignin-modulating polypeptides discussed herein fit the indicated HMM with an HMM bit score greater than 20 (e.g., greater than 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, or 500). In some embodiments, the HMM bit score of a lignin-modulating polypeptide discussed below is about 50%, 60%, 70%, 80%, 90%, or 95% of the HMM bit score of a functional homolog provided in one of FIGS. 1-22. In some embodiments, a lignin-modulating polypeptide discussed herein fits the indicated HMM with an HMM bit score greater than 20, and has a conserved domain e.g., a PFAM domain, or a conserved region having 70% or greater sequence identity (e.g., 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity) to a conserved domain or region present in a lignin-modulating polypeptide disclosed herein. In some embodiments, a lignin-modulating polypeptide discussed herein fits the indicated HMM with an HMM bit score greater than 20, and can have a conserved domain, e.g., a PFAM domain, or a conserved region having 70% or greater sequence identity (e.g., 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity) to a conserved domain or region present in a lignin-modulating polypeptide disclosed herein.

For example, a lignin-modulating polypeptide can fit an HMM generated using the amino acid sequences set forth in FIG. 1 with an HMM bit score that is greater than about 1100 (e.g., greater than about 1125, 1150, 1200, 1230, or 1250). In some cases, a protein-modulating polypeptide can fit an HMM generated using the amino acid sequences set forth in FIG. 2 with an HMM bit score that is greater than about 1275 (e.g., greater than about 1300, 1350, 1400, 1450, 1500, 1550, 1600, or 1650). In some cases, a lignin-modulating polypeptide can fit an HMM generated using the amino acid sequences set forth in FIG. 3 with an HMM bit score that is greater than about 1175 (e.g., greater than about 1200, 1225, 1250, or 1275). In some cases, a lignin-modulating polypeptide can fit an HMM generated using the amino acid sequences set forth in FIG. 4 with an HMM bit score that is greater than about 400 (e.g., greater than about 425, 450, 500, 550, 600, 650, 700, or 750). In some cases, a lignin-modulating polypeptide can fit an HMM generated using the amino acid sequences set forth in FIG. 5 with an HMM bit score that is greater than about 1000 (e.g., greater than about 1025, 1050, 1100, 1150, 1200, or 1250). In some cases, a lignin-modulating polypeptide can fit an HMM generated using the amino acid sequences set forth in FIG. 6 with an HMM bit score that is greater than about 120 (e.g., greater than about 125, 130, or 135). In some cases, a lignin-modulating polypeptide can fit an HMM generated using the amino acid sequences set forth in FIG. 7 with an HMM bit score that is greater than about 1375 (e.g., greater than about 1400, 1450, 1500, or 1520). In some cases, a lignin-modulating polypeptide can fit an HMM generated using the amino acid sequences set forth in FIG. 8 with an HMM bit score that is greater than about 1100 (e.g., greater than about 1125, 1150, 1200, or 1225). In some cases, a lignin-modulating polypeptide can fit an HMM generated using the amino acid sequences set forth in FIG. 9 with an HMM bit score that is greater than about 700 (e.g., greater than about 710, 725, 750, 775, 800, 810, or 825). In some cases, a lignin-modulating polypeptide can fit an HMM generated using the amino acid sequences set forth in FIG. 10 with an HMM bit score that is greater than about 825 (e.g., greater than about 830, 840, 850, or 860). In some cases, a lignin-modulating polypeptide can fit an HMM generated using the amino acid sequences set forth in FIG. 11 with an HMM bit score that is greater than about 530 (e.g., greater than about 540, 550, 575, or 600). In some cases, a lignin-modulating polypeptide can fit an HMM generated using the amino acid sequences set forth in FIG. 12 with an HMM bit score that is greater than about 900 (e.g., greater than about 910, 925, 950, 1000, 1050, 1100, or 1150). In some cases, a lignin-modulating polypeptide can fit an HMM generated using the amino acid sequences set forth in FIG. 13 with an HMM bit score that is greater than about 460 (e.g., greater than about 475, 500, 510, or 520). In some cases, a lignin-modulating polypeptide can fit an HMM generated using the amino acid sequences set forth in FIG. 14 with an HMM bit score that is greater than about 600 (e.g., greater than about 610, 625, 650, 660, 675, or 685). In some cases, a lignin-modulating polypeptide can fit an HMM generated using the amino acid sequences set forth in FIG. 15 with an HMM bit score that is greater than about 180 (e.g., greater than about 185, 190, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 500, 525, 550, 1150, 1200, or 1250). In some cases, a lignin-modulating polypeptide can fit an HMM generated using the amino acid sequences set forth in FIG. 16 with an HMM bit score that is greater than about 575 (e.g., greater than about 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, or 1100). In some cases, a lignin-modulating polypeptide can fit an HMM generated using the amino acid sequences set forth in FIG. 17 with an HMM bit score that is greater than about 85 (e.g., greater than about 100, 200, 300, 400, 450, 500, 600, 650, 700, 750, 800, 850, 900, 950, 1000, or 1050). In some cases, a lignin-modulating polypeptide can fit an HMM generated using the amino acid sequences set forth in FIG. 18 with an HMM bit score that is greater than about 150 (e.g., greater than about 200, 250, 300, 350, 400, 450, 500, 550, or 600). In some cases, a lignin-modulating polypeptide can fit an HMM generated using the amino acid sequences set forth in FIG. 19 with an HMM bit score that is greater than about 375 (e.g., greater than about 400, 425, 450, 475, 500, 525, 550, 575, 600, 650, 700, 750, 800, 850, 900, 950, 1000, or 1050). In some cases, a lignin-modulating polypeptide can fit an HMM generated using the amino acid sequences set forth in FIG. 20 with an HMM bit score that is greater than about 700 (e.g., greater than about 710, 725, 750, 800, 825, 850, 900, 925, 950, 1000, 1050, or 1100). In some cases, a lignin-modulating polypeptide can fit an HMM generated using the amino acid sequences set forth in FIG. 21 with an HMM bit score that is greater than about 420 (e.g., greater than about 450, 500, 550, 600, 625, 650, 675, or 700). In some cases, a lignin-modulating polypeptide can fit an HMM generated using the amino acid sequences set forth in FIG. 22 with an HMM bit score that is greater than about 375 (e.g., greater than about 380, 385, 390, or 400).

Nucleic Acids

A nucleic acid can comprise a coding sequence that encodes any of the lignin-modulating polypeptides as set forth in SEQ ID NO:96, SEQ ID NOs:98-107, SEQ ID NOs:109-111, SEQ ID NOs:113-114, SEQ ID NOs:116-124, SEQ ID NOs:126-127, SEQ ID NOs:129-130, SEQ ID NO:132, SEQ ID NO:134, SEQ ID NO:136, SEQ ID NO:138, SEQ ID NO:140, SEQ ID NOs:142-143, SEQ ID NOs:145-147, SEQ ID NOs:149-150, SEQ ID NOs:152-156, SEQ ID NO:158, SEQ ID NOs:160-163, SEQ ID NO:165, SEQ ID NOs:167-174, SEQ ID NOs:176-181, SEQ ID NO:183, SEQ ID NO:185, SEQ ID NOs:187-188, SEQ ID NO:190, SEQ ID NOs:192-194, SEQ ID NOs:196-197, SEQ ID NO:199, SEQ ID NOs:201-202, SEQ ID NO:204, SEQ ID NO:206, SEQ ID NO:208, SEQ ID NOs:210-214, SEQ ID NO:216, SEQ ID NOs:218-220, SEQ ID NO:222, SEQ ID NO:224, SEQ ID NOs:226-227, SEQ ID NO:229, SEQ ID NO:231, SEQ ID NOs:233-238, SEQ ID NO:240, SEQ ID NO:242, SEQ ID NO:244, SEQ ID NO:246, SEQ ID NO:248, SEQ ID NO:250, SEQ ID NO:252, SEQ ID NO:254, SEQ ID NOs:256-268, SEQ ID NOs:270-279, SEQ ID NOs:281-282, SEQ ID NO:284, SEQ ID NOs:286-287, SEQ ID NO:289, SEQ ID NOs:291-298, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NOs:304-309, SEQ ID NOs:311-319, SEQ ID NOs:321-330, SEQ ID NOs:332-340, SEQ ID NO:342, SEQ ED NO:344, SEQ ID NOs:355-356, SEQ ID NOs:358-369, SEQ ID NO:371, SEQ ID NOs:373-385, SEQ ID NOs:390-395, SEQ ID NO:397, SEQ ID NO:399, SEQ ID NOs:401-407, SEQ ID NOs:409-463, SEQ ID NOs:465-496, SEQ ID NOs:498-500, SEQ ID NOs:502-503, SEQ ID NO:505, SEQ ID NOs:507-511, SEQ ID NOs:513-540, SEQ ID NO:542, SEQ ID NOs:544-571, SEQ ID NOs:579-581, SEQ ID NOs:583-587, SEQ ID NOs:589-590, SEQ ID NO:592, SEQ ID NOs:595-599, SEQ ID NOs:601-617, SEQ ID NO:619, SEQ ID NOs:621-638, SEQ ID NOs:640-672, SEQ ID NO:674, SEQ ID NOs:676-678, SEQ ID NO:680, SEQ ID NOs:682-685, SEQ ID NO:687, SEQ ID NO:689, SEQ ID NOs:691-714, SEQ ID NOs:716-717, SEQ ID NOs:719-737, SEQ ID NO:739, SEQ ID NOs:741-766, SEQ ID NO:768, SEQ ID NOs:770-776, SEQ ID NO:778, SEQ ID NOs:780-786, SEQ ID NOs:788-792, SEQ ID NO:794-807, and SEQ ID NOs:809-820.

Examples of nucleic acids encoding lignin-modulating polypeptides are set forth in SEQ ID NO:95, SEQ ID NO:97, SEQ ID NO:108, SEQ ID NO:112, SEQ ID NO:115, SEQ ID NO:125, SEQ ID NO:128, SEQ ID NO:131, SEQ ID NO:133, SEQ ID NO:135, SEQ ID NO:137, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:144, SEQ ID NO:148, SEQ ID NO:151, SEQ ID NO:157, SEQ ID NO:159, SEQ ID NO:164, SEQ ID NO:166, SEQ ID NO:175, SEQ ID NO:182, SEQ ID NO:184, SEQ ID NO:186, SEQ ID NO:189, SEQ ID NO:191, SEQ ID NO:195, SEQ ID NO:198, SEQ ID NO:200, SEQ ID NO:203, SEQ ID NO:205, SEQ ID NO:207, SEQ ID NO:209, SEQ ID NO:215, SEQ ID NO:217, SEQ ID NO:221, SEQ ID NO:223, SEQ ID NO:225, SEQ ID NO:228, SEQ ID NO:230, SEQ ID NO:232, SEQ ID NO:239, SEQ ID NO:241, SEQ ID NO:243, SEQ ID NO:245, SEQ ID NO:247, SEQ ID NO:249, SEQ ID NO:251, SEQ ID NO:253, SEQ ID NO:255, SEQ ID NO:269, SEQ ID NO:280, SEQ ID NO:283, SEQ ID NO:285, SEQ ID NO:288, SEQ ID NO:290, SEQ ID NO:299, SEQ ID NO:301, SEQ ID NO:303, SEQ ID NO:310, SEQ ID NO:320, SEQ ID NO:331, SEQ ID NO:341, SEQ ID NO:343, SEQ ID NO:357, SEQ ID NO:370, SEQ ID NO:372, SEQ ID NO:386, SEQ ID NO:389, SEQ ID NO:396, SEQ ID NO:398, SEQ ID NO:400, SEQ ID NO:408, SEQ ID NO:464, SEQ ID NO:497, SEQ ID NO:501, SEQ ID NO:504, SEQ ID NO:506, SEQ ID NO:512, SEQ ID NO:541, SEQ ID NO:543, SEQ ID NO:578, SEQ ID NO:582, SEQ ID NO:584, SEQ ID NO:588, SEQ ID NO:591, SEQ ID NO:593, SEQ ID NO:600, SEQ ID NO:618, SEQ ID NO:620, SEQ ID NO:639, SEQ ID NO:673, SEQ ID NO:675, SEQ ID NO:679, SEQ ID NO:681, SEQ ID NO:686, SEQ ID NO:688, SEQ ID NO:690, SEQ ID NO:715, SEQ ID NO:718, SEQ ID NO:738, SEQ ID NO:740, SEQ ID NO:767, SEQ ID NO:769, SEQ ID NO:777, SEQ ID NO:779, SEQ ID NO:787, SEQ ID NO:793, and SEQ ID NO:808.

A nucleic acid also can be a fragment that is at least 40% (e.g., at least 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 99%) of the length of the nucleic acid set forth in SEQ ID NO:95, SEQ ID NO:97, SEQ ID NO:108, SEQ ID NO:112, SEQ ID NO:115, SEQ ID NO:125, SEQ ID NO:128, SEQ ID NO:131, SEQ ID NO:133, SEQ ID NO:135, SEQ ID NO:137, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:144, SEQ ID NO:148, SEQ ID NO:151, SEQ ID NO:157, SEQ ID NO:159, SEQ ID NO:164, SEQ ID NO:166, SEQ ID NO:175, SEQ ID NO:182, SEQ ID NO:184, SEQ ID NO:186, SEQ ID NO:189, SEQ ID NO:191, SEQ ID NO:195, SEQ ID NO:198, SEQ ID NO:200, SEQ ID NO:203, SEQ ID NO:205, SEQ ID NO:207, SEQ ID NO:209, SEQ ID NO:215, SEQ ID NO:217, SEQ ID NO:221, SEQ ID NO:223, SEQ ID NO:225, SEQ ID NO:228, SEQ ID NO:230, SEQ ID NO:232, SEQ ID NO:239, SEQ ID NO:241, SEQ ID NO:243, SEQ ID NO:245, SEQ ID NO:247, SEQ ID NO:249, SEQ ID NO:251, SEQ ID NO:253, SEQ ID NO:255, SEQ ID NO:269, SEQ ID NO:280, SEQ ID NO:283, SEQ ID NO:285, SEQ ID NO:288, SEQ ID NO:290, SEQ ID NO:299, SEQ ID NO:301, SEQ ID NO:303, SEQ ID NO:310, SEQ ID NO:320, SEQ ID NO:331, SEQ ID NO:341, SEQ ID NO:343, SEQ ID NO:357, SEQ ID NO:370, SEQ ID NO:372, SEQ ID NO:386, SEQ ID NO:389, SEQ ID NO:396, SEQ ID NO:398, SEQ ID NO:400, SEQ ID NO:408, SEQ ID NO:464, SEQ ID NO:497, SEQ ID NO:501, SEQ ID NO:504, SEQ ID NO:506, SEQ ID NO:512, SEQ ID NO:541, SEQ ID NO:543, SEQ ID NO:578, SEQ ID NO:582, SEQ ID NO:584, SEQ ID NO:588, SEQ ID NO:591, SEQ ID NO:593, SEQ ID NO:600, SEQ ID NO:618, SEQ ID NO:620, SEQ ID NO:639, SEQ ID NO:673, SEQ ID NO:675, SEQ ID NO:679, SEQ ID NO:681, SEQ ID NO:686, SEQ ID NO:688, SEQ ID NO:690, SEQ ID NO:715, SEQ ID NO:718, SEQ ID NO:738, SEQ ID NO:740, SEQ ID NO:767, SEQ ID NO:769, SEQ ID NO:777, SEQ ID NO:779, SEQ ID NO:787, SEQ ID NO:793, and SEQ ID NO:808.

SEQ ID NO:108 is predicted to encode a polypeptide having the amino acid sequence set forth in SEQ ID NO:109. SEQ ID NO:112 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:113. SEQ ID NO:115 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:116. SEQ ID NO:128 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:129. SEQ ID NO:131 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:132. SEQ ID NO:137 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:138. SEQ ID NO:139 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:140. SEQ ID NO:141 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:142. SEQ ID NO:144 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:145. SEQ ID NO:151 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:152. SEQ ID NO:157 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:158. SEQ ID NO:164 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:165. SEQ ID NO:166 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:167. SEQ ID NO:184 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:185. SEQ ID NO:186 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:187. SEQ ID NO:198 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:199. SEQ ID NO:200 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:201. SEQ ID NO:205 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:206. SEQ ID NO:207 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:208. SEQ ID NO:209 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:210. SEQ ID NO:223 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:224. SEQ ID NO:228 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:229. SEQ ID NO:230 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:231. SEQ ID NO:232 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:233. SEQ ID NO:241 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:242. SEQ ID NO:243 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:244. SEQ ID NO:245 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:246. SEQ ID NO:247 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:248. SEQ ID NO:249 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:250. SEQ ID NO:251 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:252. SEQ ID NO:253 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:254. SEQ ID NO:255 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:256. SEQ ID NO:269 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ FD NO:270. SEQ ID NO:299 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:300. SEQ ID NO:301 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:302. SEQ ID NO:303 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:304. SEQ ID NO:310 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:311. SEQ ID NO:320 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:321. SEQ ID NO:331 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:332. SEQ ID NO:341 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:342. SEQ ID NO:343 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:344. SEQ ID NO:357 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:358. SEQ ID NO:370 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:371. SEQ ID NO:372 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:373. SEQ ID NO:386 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:387. SEQ ID NO:389 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:390. SEQ ID NO:396 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:397. SEQ ID NO:398 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:399. SEQ ID NO:400 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:401. SEQ ID NO:408 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:409. SEQ ID NO:464 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:465. SEQ ID NO:497 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:498. SEQ ID NO:501 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:502. SEQ ID NO:504 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:505. SEQ ID NO:506 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:507. SEQ ID NO:512 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:513. SEQ ID NO:541 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:542. SEQ ID NO:543 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:544. SEQ ID NO:578 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:579. SEQ ID NO:582 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:583. SEQ ID NO:584 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:585. SEQ ID NO:591 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:592. SEQ ID NO:593 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:594. SEQ ID NO:600 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:601. SEQ ID NO:618 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:619. SEQ ID NO:620 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:621. SEQ ID NO:639 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:640. SEQ ID NO:673 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:674. SEQ ID NO:675 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:676. SEQ ID NO:679 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:680. SEQ ID NO:681 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:682. SEQ ID NO:686 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:687. SEQ ID NO:688 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:689. SEQ ID NO:690 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:691. SEQ ID NO:715 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:716. SEQ ID NO:718 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:719. SEQ ID NO:738 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:739. SEQ ID NO:740 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:741. SEQ ID NO:767 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:768. SEQ ID NO:769 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:770. SEQ ID NO:777 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:778. SEQ ID NO:779 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:780. SEQ ID NO:787 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:788. SEQ ID NO:793 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:795. SEQ ID NO:808 is predicted to encode the polypeptide having the amino acid sequence set forth in SEQ ID NO:809.

In some cases, a recombinant nucleic acid construct can include a nucleic acid comprising less than the full-length coding sequence of a lignin-modulating polypeptide. In some cases, a recombinant nucleic acid construct can include a nucleic acid comprising a coding sequence, a gene, or a fragment of a coding sequence or gene in an antisense orientation so that the antisense strand of RNA is transcribed.

It will be appreciated that a number of nucleic acids can encode a polypeptide having a particular amino acid sequence. The degeneracy of the genetic code is well known to the art; i.e., for many amino acids, there is more than one nucleotide triplet that serves as the codon for the amino acid. For example, codons in the coding sequence for a given lignin-modulating polypeptide can be modified such that optimal expression in a particular plant species is obtained, using appropriate codon bias tables for that species.

A nucleic acid also can comprise a nucleotide sequence corresponding to any of the regulatory regions as set forth in SEQ ID NOs:1-94 or SEQ ID NOs:345-354. In some cases, a nucleic acid can comprise a nucleotide sequence corresponding to any of the regulatory regions set forth in SEQ ID NOs:1-94 or SEQ ID NOs:345-354, and a coding sequence that encodes any of the lignin-modulating polypeptides set forth in SEQ ID NO:96, SEQ ID NOs:98-107, SEQ ID NOs:109-111, SEQ ID NOs:113-114, SEQ ID NOs:116-124, SEQ ID NOs:126-127, SEQ ID NOs:129-130, SEQ ID NO:132, SEQ ID NO:134, SEQ ID NO:136, SEQ ID NO:138, SEQ ID NO:140, SEQ ID NOs:142-143, SEQ ID NOs:145-147, SEQ ID NOs:149-150, SEQ ID NOs:152-156, SEQ ID NO:158, SEQ ID NOs:160-163, SEQ ID NO:165, SEQ ID NOs:167-174, SEQ ID NOs:176-181, SEQ ID NO:183, SEQ ID NO:185, SEQ ID NOs:187-188, SEQ ID NO:190, SEQ ID NOs:192-194, SEQ ID NOs:196-197, SEQ ID NO:199, SEQ ID NOs:201-202, SEQ ID NO:204, SEQ ID NO:206, SEQ ID NO:208, SEQ ID NOs:210-214, SEQ ID NO:216, SEQ ID NOs:218-220, SEQ ID NO:222, SEQ ID NO:224, SEQ ID NOs:226-227, SEQ ID NO:229, SEQ ID NO:231, SEQ ID NOs:233-238, SEQ ID NO:240, SEQ ID NO:242, SEQ ID NO:244, SEQ ID NO:246, SEQ ID NO:248, SEQ ID NO:250, SEQ ID NO:252, SEQ ID NO:254, SEQ ID NOs:256-268, SEQ ID NOs:270-279, SEQ ID NOs:281-282, SEQ ID NO:284, SEQ ID NOs:286-287, SEQ ID NO:289, SEQ ID NOs:291-298, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NOs:304-309, SEQ ID NOs:311-319, SEQ ID NOs:321-330, SEQ ID NOs:332-340, SEQ ID NO:342, SEQ ID NO:344, SEQ ID NOs:355-356, SEQ ID NOs:358-369, SEQ ID NO:371, SEQ ID NOs:373-385, SEQ ID NOs:390-395, SEQ ID NO:397, SEQ ID NO:399, SEQ ID NOs:401-407, SEQ ID NOs:409-463, SEQ ID NOs:465-496, SEQ ID NOs:498-500, SEQ ID NOs:502-503, SEQ ID NO:505, SEQ ID NOs:507-511, SEQ ID NOs:513-540, SEQ ID NO:542, SEQ ID NOs:544-571, SEQ ID NOs:579-581, SEQ ID NOs:583-587, SEQ ID NOs:589-590, SEQ ID NO:592, SEQ ID NOs:595-599, SEQ ID NOs:601-617, SEQ ID NO:619, SEQ ID NOs:621-638, SEQ ID NOs:640-672, SEQ ID NO:674, SEQ ID NOs:676-678, SEQ ID NO:680, SEQ ID NOs:682-685, SEQ ID NO:687, SEQ ID NO:689, SEQ ID NOs:691-714, SEQ ID NOs:716-717, SEQ ID NOs:719-737, SEQ ID NO:739, SEQ ID NOs:741-766, SEQ ID NO:768, SEQ ID NOs:770-776, SEQ ID NO:778, SEQ ID NOs:780-786, SEQ ID NOs:788-792, SEQ ID NO:794-807, and SEQ ID NOs:809-820.

The terms “nucleic acid” and “polynucleotide” are used interchangeably herein, and refer both to RNA and DNA, including cDNA, genomic DNA, synthetic DNA, and DNA (or RNA) containing nucleic acid analogs. Polynucleotides can have any three-dimensional structure. A nucleic acid can be double-stranded or single-stranded (i.e., a sense strand or an antisense strand). Non-limiting examples of polynucleotides include genes, gene fragments, exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA, siRNA, micro-RNA, ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers, as well as nucleic acid analogs.

An isolated nucleic acid can be, for example, a naturally-occurring DNA molecule, provided one of the nucleic acid sequences normally found immediately flanking that DNA molecule in a naturally-occurring genome is removed or absent. Thus, an isolated nucleic acid includes, without limitation, a DNA molecule that exists as a separate molecule, independent of other sequences (e.g., a chemically synthesized nucleic acid, or a cDNA or genomic DNA fragment produced by the polymerase chain reaction (PCR) or restriction endonuclease treatment). An isolated nucleic acid also refers to a DNA molecule that is incorporated into a vector, an autonomously replicating plasmid, a virus, or into the genomic DNA of a prokaryote or eukaryote. In addition, an isolated nucleic acid can include an engineered nucleic acid such as a DNA molecule that is part of a hybrid or fusion nucleic acid. A nucleic acid existing among hundreds to millions of other nucleic acids within, for example, cDNA libraries or genomic libraries, or gel slices containing a genomic DNA restriction digest, is not to be considered an isolated nucleic acid.

Isolated nucleic acid molecules can be produced by standard techniques. For example, polymerase chain reaction (PCR) techniques can be used to obtain an isolated nucleic acid containing a nucleotide sequence described herein. PCR can be used to amplify specific sequences from DNA as well as RNA, including sequences from total genomic DNA or total cellular RNA. Various PCR methods are described, for example, in PCR Primer: A Laboratory Manual, Dieffenbach and Dveksler, eds., Cold Spring Harbor Laboratory Press, 1995. Generally, sequence information from the ends of the region of interest or beyond is employed to design oligonucleotide primers that are identical or similar in sequence to opposite strands of the template to be amplified. Various PCR strategies also are available by which site-specific nucleotide sequence modifications can be introduced into a template nucleic acid. Isolated nucleic acids also can be chemically synthesized, either as a single nucleic acid molecule (e.g., using automated DNA synthesis in the 3′ to 5′ direction using phosphoramidite technology) or as a series of oligonucleotides. For example, one or more pairs of long oligonucleotides (e.g., >100 nucleotides) can be synthesized that contain the desired sequence, with each pair containing a short segment of complementarity (e.g., about 15 nucleotides) such that a duplex is formed when the oligonucleotide pair is annealed. DNA polymerase is used to extend the oligonucleotides, resulting in a single, double-stranded nucleic acid molecule per oligonucleotide pair, which then can be ligated into a vector. Isolated nucleic acids of the invention also can be obtained by mutagenesis of, e.g., a naturally occurring DNA.

As used herein, the term “percent sequence identity” refers to the degree of identity between any given query sequence and a subject sequence. A subject sequence typically has a length that is more than 80%, e.g., more than 82%, 85%, 87%, 89%, 90%, 93%, 95%, 97%, 99%, 100%, 105%, 110%, 115%, or 120%, of the length of the query sequence. A query nucleic acid or amino acid sequence is aligned to one or more subject nucleic acid or amino acid sequences using the computer program ClustalW (version 1.83, default parameters), which allows alignments of nucleic acid or protein sequences to be carried out across their entire length (global alignment). Chenna et al., Nucleic Acids Res., 31(13):3497-500 (2003).

ClustalW calculates the best match between a query and one or more subject sequences, and aligns them so that identities, similarities and differences can be determined. Gaps of one or more residues can be inserted into a query sequence, a Subject sequence, or both, to maximize sequence alignments. For fast pairwise alignment of nucleic acid sequences, the following default parameters are used: word size: 2; window size: 4; scoring method: percentage; number of top diagonals: 4; and gap penalty: 5. For multiple alignment of nucleic acid sequences, the following parameters are used: gap opening penalty: 10.0; gap extension penalty: 5.0; and weight transitions: yes. For fast pairwise alignment of protein sequences, the following parameters are used: word size: 1; window size: 5; scoring method: percentage; number of top diagonals: 5; gap penalty: 3. For multiple alignment of protein sequences, the following parameters are used: weight matrix: blosum; gap opening penalty: 10.0; gap extension penalty: 0.05; hydrophilic gaps: on; hydrophilic residues: Gly, Pro, Ser, Asn, Asp, Gln, Glu, Arg, and Lys; residue-specific gap penalties: on. The output is a sequence alignment that reflects the relationship between sequences. ClustalW can be run, for example, at the Baylor College of Medicine Search Launcher site (searchlauncher.bcm.tmc.edu/multi-align/multi-align.html) and at the European Bioinformatics Institute site on the World Wide Web (ebi.ac.uk/clustalw).

To determine a percent identity between a query sequence and a subject sequence, ClustalW divides the number of identities in the best alignment by the number of residues compared (gap positions are excluded), and multiplies the result by 100. The output is the percent identity of the subject sequence with respect to the query sequence. It is noted that the percent identity value can be rounded to the nearest tenth. For example, 78.11, 78.12, 78.13, and 78.14 are rounded down to 78.1, while 78.15, 78.16, 78.17, 78.18, and 78.19 are rounded up to 78.2.

The term “exogenous” with respect to a nucleic acid indicates that the nucleic acid is part of a recombinant nucleic acid construct, or is not in its natural environment. For example, an exogenous nucleic acid can be a sequence from one species introduced into another species, i.e., a heterologous nucleic acid. Typically, such an exogenous nucleic acid is introduced into the other species via a recombinant nucleic acid construct. An exogenous nucleic acid can also be a sequence that is native to an organism and that has been reintroduced into cells of that organism. An exogenous nucleic acid that includes a native sequence can often be distinguished from the naturally occurring sequence by the presence of non-natural sequences linked to the exogenous nucleic acid, e.g., non-native regulatory sequences flanking a native sequence in a recombinant nucleic acid construct. In addition, stably transformed exogenous nucleic acids typically are integrated at positions other than the position where the native sequence is found. It will be appreciated that an exogenous nucleic acid may have been introduced into a progenitor and not into the cell under consideration. For example, a transgenic plant containing an exogenous nucleic acid can be the progeny of a cross between a stably transformed plant and a non-transgenic plant. Such progeny are considered to contain the exogenous nucleic acid.

Similarly, a lignin-modulating polypeptide can be endogenous or exogenous to a particular plant or plant cell. Exogenous lignin-modulating polypeptides, therefore, can include proteins that are native to a plant or plant cell, but that are expressed in a plant cell via a recombinant nucleic acid construct, e.g., a Panicum plant transformed with a recombinant nucleic acid construct encoding a Panicum transcription factor.

Likewise, a regulatory region can be exogenous or endogenous to a plant or plant cell. An exogenous regulatory region is a regulatory region that is part of a recombinant nucleic acid construct, or is not in its natural environment. For example, a Nicotiana promoter present on a recombinant nucleic acid construct is an exogenous regulatory region when a Nicotiana plant cell is transformed with the construct.

A transgenic plant or plant cell in which the amount and/or rate of biosynthesis of one or more sequences of interest is modulated includes at least one recombinant nucleic acid construct, e.g., a nucleic acid construct comprising a nucleic acid encoding a lignin-modulating polypeptide as described herein. In certain cases, more than one recombinant nucleic acid construct can be included (e.g., two, three, four, five, six, or more recombinant nucleic acid constructs). For example, two recombinant nucleic acid constructs can be included, where one construct includes a nucleic acid encoding one lignin-modulating polypeptide, and another construct includes a nucleic acid encoding a second lignin-modulating polypeptide.

Vectors containing nucleic acids such as those described herein also are provided. A “vector” is a replicon, such as a plasmid, phage, or cosmid, into which another DNA segment may be inserted so as to bring about the replication of the inserted segment. Generally, a vector is capable of replication when associated with the proper control elements. Suitable vector backbones include, for example, those routinely used in the art such as plasmids, viruses, artificial chromosomes, BACs, YACs, or PACs. The term “vector” includes cloning and expression vectors, as well as viral vectors and integrating vectors. An “expression vector” is a vector that includes a regulatory region. Suitable expression vectors include, without limitation, plasmids and viral vectors derived from, for example, bacteriophage, baculoviruses, and retroviruses. Numerous vectors and expression systems are commercially available from such corporations as Novagen (Madison, Wis.), Clontech (Mountain View, Calif.), Stratagene (La Jolla, Calif.), and Invitrogen/Life Technologies (Carlsbad, Calif.).

The vectors provided herein also can include, for example, origins of replication, scaffold attachment regions (SARs), and/or markers. A marker gene can confer a selectable phenotype on a plant cell. For example, a marker can confer biocide resistance, such as resistance to an antibiotic (e.g., kanamycin, G418, bleomycin, or hygromycin), or an herbicide (e.g., chlorosulfuron or phosphinothricin). In addition, an expression vector can include a tag sequence designed to facilitate manipulation or detection (e.g., purification or localization) of the expressed polypeptide. Tag sequences, such as green fluorescent protein (GFP), glutathione S-transferase (GST), polyhistidine, c-myc, hemagglutinin, or Flag™ tag (Kodak, New Haven, Conn.) sequences typically are expressed as a fusion with the encoded polypeptide. Such tags can be inserted anywhere within the polypeptide, including at either the carboxyl or amino terminus. As described herein, plant cells can be transformed with a recombinant nucleic acid construct to express a polypeptide of interest.

Regulatory Regions

The term “regulatory region” refers to a nucleic acid having nucleotide sequences that influence transcription or translation initiation and rate, and stability and/or mobility of a transcription or translation product. Regulatory regions include, without limitation, promoter sequences, enhancer sequences, response elements, protein recognition sites, inducible elements, protein binding sequences, 5′ and 3′ untranslated regions (UTRs), transcriptional start sites, termination sequences, polyadenylation sequences, introns, and combinations thereof.

As used herein, the term “operably linked” refers to positioning of a regulatory region and a sequence to be transcribed in a nucleic acid so as to influence transcription or translation of such a sequence. For example, to bring a coding sequence under the control of a regulatory region, the translation initiation site of the translational reading frame of the polypeptide is typically positioned between one and about fifty nucleotides downstream of the promoter. A regulatory region can, however, be positioned as much as about 5,000 nucleotides upstream of the translation initiation site, or about 2,000 nucleotides upstream of the transcription start site. A regulatory region typically comprises at least a core (basal) promoter. A regulatory region also may include at least one control element, such as an enhancer sequence, an upstream element or an upstream activation region (UAR). For example, a suitable enhancer is a cis-regulatory element (−212 to −154) from the upstream region of the octopine synthase (ocs) gene. Fromm et al., The Plant Cell, 1:977-984 (1989). The choice of regulatory regions to be included depends upon several factors, including, but not limited to, efficiency, selectability, inducibility, desired expression level, and cell- or tissue-preferential expression. It is a routine matter for one of skill in the art to modulate the expression of a coding sequence by appropriately selecting and positioning regulatory regions relative to the coding sequence.

Some suitable regulatory regions initiate transcription only, or predominantly, in certain cell types. For example, a promoter that is active predominantly in a reproductive tissue (e.g., fruit, ovule, or inflorescence) can be used. Thus, as used herein a cell type- or tissue-preferential promoter is one that drives expression preferentially in the target tissue, but may also lead to some expression in other cell types or tissues as well. Methods for identifying and characterizing regulatory regions in plant genomic DNA include, for example, those described in the following references: Jordano et al., Plant Cell, 1:855-866 (1989); Bustos et al., Plant Cell, 1:839-854 (1989); Green et al., EMBO J., 7:4035-4044 (1988); Meier et al., Plant Cell, 3:309-316 (1991); and Zhang et al., Plant Physiology, 110: 1069-1079 (1996).

Examples of various classes of regulatory regions are described below. Some of the regulatory regions indicated below as well as additional regulatory regions are described in more detail in U.S. Patent Application Ser. Nos. 60/505,689; 60/518,075; 60/544,771; 60/558,869; 60/583,691; 60/619,181; 60/637,140; 60/757,544; 60/776,307; 10/957,569; Ser. Nos. 11/058,689; 11/172,703; 11/208,308; 11/274,890; 60/583,609; 60/612,891; Ser. Nos. 11/097,589; 11/233,726; 11/408,791; 11/414,142; 10/950,321; 11/360,017; PCT/US05/011105; PCT/US05/034308; and PCT/US05/23639. Nucleotide sequences of regulatory regions are set forth in SEQ ID NOs:1-94 and SEQ ID NOs:345-354. It will be appreciated that a regulatory region may meet criteria for one classification based on its activity in one plant species, and yet meet criteria for a different classification based on its activity in another plant species.

Broadly Expressing Promoters

A promoter can be said to be “broadly expressing” when it promotes transcription in many, but not necessarily all, plant tissues. For example, a broadly expressing promoter can promote transcription of an operably linked sequence in one or more of the shoot, shoot tip (apex), and leaves, but weakly or not at all in tissues such as roots or stems. As another example, a broadly expressing promoter can promote transcription of an operably linked sequence in one or more of the stem, shoot, shoot tip (apex), and leaves, but can promote transcription weakly or not at all in tissues such as reproductive tissues of flowers and developing seeds. Non-limiting examples of broadly expressing promoters that can be included in the nucleic acid constructs provided herein include the p326 (SEQ ID NO:76), YP0144 (SEQ ID NO:54), YP0190 (SEQ ID NO:59), p13879 (SEQ ID NO:75), YP0050 (SEQ ID NO:35), p32449 (SEQ ID NO:77), 21876 (SEQ ID NO:1), YP0158 (SEQ ID NO:57), YP0214 (SEQ ID NO:61), YP0380 (SEQ ID NO:70), PT0848 (SEQ ID NO:26), and PT0633 (SEQ ID NO:7) promoters. Additional examples include the cauliflower mosaic virus (CaMV) 35S promoter, the mannopine synthase (MAS) promoter, the 1′ or 2′ promoters derived from T-DNA of Agrobacterium tumefaciens, the figwort mosaic virus 34S promoter, actin promoters such as the rice actin promoter, and ubiquitin promoters such as the maize ubiquitin-1 promoter. In some cases, the CaMV 35S promoter is excluded from the category of broadly expressing promoters.

Root Promoters

Root-active promoters confer transcription in root tissue, e.g., root endodermis, root epidermis, or root vascular tissues. In some embodiments, root-active promoters are root-preferential promoters, i.e., confer transcription only or predominantly in root tissue. Root-preferential promoters include the YP0128 (SEQ ID NO:52), YP0275 (SEQ ID NO:63), PT0625 (SEQ ID NO:6), PT0660 (SEQ ID NO:9), PT0683 (SEQ ID NO:14), and PT0758 (SEQ ID NO:22) promoters. Other root-preferential promoters include the PT0613 (SEQ ID NO:5), PT0672 (SEQ ID NO:11), PT0688 (SEQ ID NO:15), and PT0837 (SEQ ID NO:24) promoters, which drive transcription primarily in root tissue and to a lesser extent in ovules and/or seeds. Other examples of root-preferential promoters include the root-specific subdomains of the CaMV 35S promoter (Lam et al., Proc. Natl. Acad. Sci. USA, 86:7890-7894 (1989)), root cell specific promoters reported by Conkling et al., Plant Physiol., 93:1203-1211 (1990), and the tobacco RD2 promoter.

Ovary Tissue Promoters

Promoters that are active in ovary tissues such as the ovule wall and mesocarp can also be useful, e.g., a polygalacturonidase promoter, the banana TRX promloter, the melon actin promoter, YP0396 (SEQ ID NO:74), and PT0623 (SEQ ID NO:94). Examples of promoters that are active primarily in ovules include YP0007 (SEQ ID NO:30), YP0111 (SEQ ID NO:46), YP0092 (SEQ ID NO:38), YP0103 (SEQ ID NO:43), YP0028 (SEQ ID NO:33), YP0121 (SEQ ID NO:51), YP0008 (SEQ ID NO:31), YP0039 (SEQ ID NO:34), YP0115 (SEQ ID NO:47), YP0119 (SEQ ID NO:49), YP0120 (SEQ ID NO:50), and YP0374 (SEQ ID NO:68).

Photosynthetic Tissue Promoters

Promoters active in photosynthetic tissue confer transcription in green tissues such as leaves and stems. Most suitable are promoters that drive expression only or predominantly in such tissues. Examples of such promoters include the ribulose-1,5-bisphosphate carboxylase (RbcS) promoters such as the RbcS promoter from eastern larch (Larix laricina), the pine cab6 promoter (Yamamoto et al., Plant Cell Physiol., 35:773-778 (1994)), the Cab-1 promoter from wheat (Fejes et al., Plant Mol. Biol., 15:921-932 (1990)), the CAB-1 promoter from spinach (Lubberstedt et al., Plant Physiol., 104:997-1006 (1994)), the cab1R promoter from rice (Luan et al., Plant Cell, 4:971-981 (1992)), the pyruvate orthophosphate dikinase (PPDK) promoter from corn (Matsuoka et al., Proc. Natl. Acad. Sci. USA, 90:9586-9590 (1993)), the tobacco Lhcb1*2 promoter (Cerdan et al., Plant Mol. Biol., 33:245-255 (1997)), the Arabidopsis thaliana SUC2 sucrose-H⁺ symporter promoter (Truernit et al., Planta, 196:564-570 (1995)), and thylakoid membrane protein promoters from spinach (psaD, psaF, psaE, PC, FNR, atpC, atpD, cab, rbcS). Other photosynthetic tissue promoters include PT0535 (SEQ ID NO:3), PT0668 (SEQ ID NO:2), PT0886 (SEQ ID NO:29), YP0144 (SEQ ID NO:55), YP0380 (SEQ ID NO:70), and PT0585 (SEQ ID NO:4).

Lignin Biosynthesis Promoters

Lignin biosynthesis promoters are promoters that drive transcription of nucleic acids encoding enzymes involved in lignin biosynthesis. Such enzymes include, without limitation, 4-(hydroxy)cinnamoyl CoA ligase (EC 6.2.1.12), ferulate 5-hydroxylase, cinnamoyl CoA reductase (EC 1.2.1.44), cinnamate 4-hydroxylase (EC 1.14.13.11), and cinnamyl alcohol dehydrogenase (EC 1.1.1.195). Examples of lignin biosynthesis promoters from Populus are set forth in SEQ ID NOs:345-354. Other examples of lignin biosynthesis promoters include promoters of the switchgrass (Panicum virgatum), rice (Oryza sativa), corn (Zea mays), and wheat (Triticum aestivum) homologs of the Populus cinnamate 4-hydroxylase, caffeoyl-CoA O-methyltransferase, and caffeic acid O-methyltransferase genes. Also suitable are promoters of Arabidopsis genes encoding phenylalanin ammonia lyase (genomic locus At3g10340), trans-cinnamate 4-hydroxylase (genomic locus At2g30490), 4-coumarate:CoA ligase (genomic locus At1g51680), hydroxycinnamoyl-CoA:shikimate/quinate hydroxycinnamoyltransferase (genomic locus At5g48930), p-Coumarate 3-hydroxylase (genomic locus At2g40890), caffeoyl-CoA 3-O-methyltransferase (genomic locus At4g34050), cinnamoyl CoA reductase (genomic locus At1g15950), ferulate 5-hydroxylase (genomic locus At4g36220), caffeic acid O-methyltransferase (genomic locus At5g54160), and cinnamyl alcohol dehydrogenase (genomic locus At4g34230).

Cell Wall Related Promoters

Useful promoters also include cell wall related promoters, such as cellulose biosynthesis promoters. Cellulose biosynthesis promoters are promoters that drive transcription of nucleic acids encoding enzymes involved in cellulose biosynthesis. Examples of cellulose biosynthesis promoters include the promoter of the rice cellulose synthase gene (genomic locus Os08g25710), the promoter of the rice cellulose synthase gene (genomic locus Os08g06380), and the promoter of the rice cellulose synthase-like A2 gene (genomic locus Os10g26630).

Vascular Tissue Promoters

Examples of promoters that have high or preferential activity in vascular bundles include YP0087 (SEQ ID NO:86), YP0093 (SEQ ID NO:87), YP0108 (SEQ ID NO:88), YP0022 (SEQ ID NO:89), and YP0080 (SEQ ID NO:90). Other vascular tissue-preferential promoters include the glycine-rich cell wall protein GRP 1.8 promoter (Keller and Baumgartner, Plant Cell, 3(10):1051-1061 (1991)), the Commelina yellow mottle virus (CoYMV) promoter (Medberry et al., Plant Cell, 4(2):185-192 (1992)), and the rice tungro bacilliform virus (RTBV) promoter (Dai et al., Proc. Natl. Acad. Sci. USA, 101(2):687-692 (2004)). Promoters having preferential activity in the phloem region (e.g., primary phloem cells, companion cells, and sieve cells), the xylem region (e.g., tracheids and vessels), the bundle sheath layer and/or the endodermis are also considered vascular tissue promoters.

Stem Promoters

Promoters that have preferential activity in the pith, cortex, epidermis, and/or in the vascular bundles or vascular layers of the stem are considered stem promoters. Examples of these promoters are YP0356 (SEQ ID NO:67), YP0108 (SEQ ID NO:88), PT0684, PT0565 (SEQ ID NO:84), PT0710 (SEQ ID NO:18), and YP0080 (SEQ ID NO:90). In some cases, the stem promoters can also be induced by stress like drought (e.g., YP0356 and PT0710).

Inducible Promoters

Inducible promoters confer transcription in response to external stimuli such as chemical agents or environmental stimuli. For example, inducible promoters can confer transcription in response to hormones such as giberellic acid or ethylene, or in response to light or drought. Examples of drought-inducible promoters include YP0380 (SEQ ID NO:70), PT0848 (SEQ ID NO:26), YP0381 (SEQ ID NO:71), YP0337 (SEQ ID NO:66), PT0633 (SEQ ID NO:7), YP0374 (SEQ ID NO:68), PT0710 (SEQ ID NO:18), YP0356 (SEQ ID NO:67), YP0385 (SEQ ID NO:73), YP0396 (SEQ ID NO:74), YP0388 (SEQ ID NO:92), YP0384 (SEQ ID NO:72), PT0688 (SEQ ID NO:15), YP0286 (SEQ ID NO:65), YP0377 (SEQ ID NO:69), PD1367 (SEQ ID NO:78), and PD0901 (SEQ ID NO:93). Examples of nitrogen-inducible promoters include PT0863 (SEQ ID NO:27), PT0829 (SEQ ID NO:23), PT0665 (SEQ ID NO:10), and PT0886 (SEQ ID NO:29). Examples of shade-inducible promoters include PR0924 (SEQ ID NO:91) and PT0678 (SEQ ID NO:13).

Basal Promoters

A basal promoter is the minimal sequence necessary for assembly of a transcription complex required for transcription initiation. Basal promoters frequently include a “TATA box” element that may be located between about 15 and about 35 nucleotides upstream from the site of transcription initiation. Basal promoters also may include a “CCAAT box” element (typically the sequence CCAAT) and/or a GGGCG sequence, which can be located between about 40 and about 200 nucleotides, typically about 60 to about 120 nucleotides, upstream from the transcription start site.

Other Promoters

Other classes of promoters include, but are not limited to, shoot-preferential, callus-preferential, trichome cell-preferential, guard cell-preferential such as PT0678 (SEQ ID NO:13), tuber-preferential, parenchyma cell-preferential, and senescence-preferential promoters. Promoters designated YP0086 (SEQ ID NO:36), YP0188 (SEQ ID NO:58), YP0263 (SEQ ID NO:62), PT0758 (SEQ ID NO:22), PT0743 (SEQ ID NO:21), PT0829 (SEQ ID NO:23), YP0119 (SEQ ID NO:49), and YP0096 (SEQ ID NO:39), as described in the above-referenced patent applications, may also be useful.

Other Regulatory Regions

A 5′ untranslated region (UTR) can be included in nucleic acid constructs described herein. A 5′ UTR is transcribed, but is not translated, and lies between the start site of the transcript and the translation initiation codon and may include the +1 nucleotide. A 3′ UTR can be positioned between the translation termination codon and the end of the transcript. UTRs can have particular functions such as increasing mRNA stability or attenuating translation. Examples of 3′ UTRs include, but are not limited to, polyadenylation signals and transcription termination sequences, e.g., a nopaline synthase termination sequence.

It will be understood that more than one regulatory region may be present in a recombinant polynucleotide, e.g., introns, enhancers, upstream activation regions, transcription terminators, and inducible elements. Thus, for example, more than one regulatory region can be operably linked to the sequence of a polynucleotide encoding a lignin-modulating polypeptide.

Regulatory regions, such as promoters for endogenous genes, can be obtained by chemical synthesis or by subcloning from a genomic DNA that includes such a regulatory region. A nucleic acid comprising such a regulatory region can also include flanking sequences that contain restriction enzyme sites that facilitate subsequent manipulation.

Methods of Inhibiting Expression of a Sequence of Interest

The polynucleotides and recombinant vectors described herein can be used to express or inhibit expression of a gene, such as an endogenous gene involved in lignin biosynthesis, e.g., to alter a lignin biosynthetic pathway in a plant species of interest. The term “expression” refers to the process of converting genetic information of a polynucleotide into RNA through transcription, which is catalyzed by an enzyme, RNA polymerase, and into protein, through translation of mRNA on ribosomes. “Up-regulation” or “activation” refers to regulation that increases the production of expression products (mRNA, polypeptide, or both) relative to basal or native states, while “down-regulation” or “repression” refers to regulation that decreases production of expression products (mRNA, polypeptide, or both) relative to basal or native states.

“Modulated level of gene expression” as used herein refers to a comparison of the level of expression of a transcript of a gene or the amount of its corresponding polypeptide in the presence and absence of a lignin-modulating polypeptide described herein, and refers to a measurable or observable change in the level of expression of a transcript of a gene or the amount of its corresponding polypeptide relative to a control plant or plant cell under the same conditions (e.g., as measured through a suitable assay such as quantitative RT-PCR, a Northern blot, a Western blot, or through an observable change in phenotype, chemical profile, or metabolic profile). A modulated level of gene expression can include up-regulated or down-regulated expression of a transcript of a gene or polypeptide relative to a control plant or plant cell under the same conditions. Modulated expression levels can occur under different environmental or developmental conditions or in different locations than those exhibited by a plant or plant cell in its native state.

A number of nucleic acid based methods, including antisense RNA, ribozyme directed RNA cleavage, post-transcriptional gene silencing (PTGS), e.g., RNA interference (RNAi), and transcriptional gene silencing (TGS) can be used to inhibit gene expression in plants. Suitable polynucleotides include full-length nucleic acids encoding lignin-modulating polypeptides, or fragments of such full-length nucleic acids. In some embodiments, a complement of the full-length nucleic acid or a fragment thereof can be used. Typically, a fragment is at least 10 nucleotides, e.g., at least 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 35, 40, 50, 80, 100, 200, 500 nucleotides or more. Generally, higher homology can be used to compensate for the use of a shorter sequence.

Antisense technology is one well-known method. In this method, a nucleic acid segment from a gene to be repressed is cloned and operably linked to a regulatory region and a transcription termination sequence so that the antisense strand of RNA is transcribed. The recombinant vector is then transformed into plants, as described below, and the antisense strand of RNA is produced. The nucleic acid segment need not be the entire sequence of the gene to be repressed, but typically will be substantially complementary to at least a portion of the sense strand of the gene to be repressed.

In another method, a nucleic acid can be transcribed into a ribozyme, or catalytic RNA, that affects expression of an mRNA. See, U.S. Pat. No. 6,423,885. Ribozymes can be designed to specifically pair with virtually any target RNA and cleave the phosphodiester backbone at a specific location, thereby functionally inactivating the target RNA. Heterologous nucleic acids can encode ribozymes designed to cleave particular mRNA transcripts, thus preventing expression of a polypeptide. Hammerhead ribozymes are useful for destroying particular mRNAs, although various ribozymes that cleave mRNA at site-specific recognition sequences can be used. Hammerhead ribozymes cleave mRNAs at locations dictated by flanking regions that form complementary base pairs with the target mRNA. The sole requirement is that the target RNA contain a 5′-UG-3′ nucleotide sequence. The construction and production of hammerhead ribozymes is known in the art. See, for example, U.S. Pat. No. 5,254,678 and WO 02/46449 and references cited therein. Hammerhead ribozyme sequences can be embedded in a stable RNA such as a transfer RNA (tRNA) to increase cleavage efficiency in vivo. Perriman et al., Proc. Natl. Acad. Sci. USA, 92(13):6175-6179 (1995); de Feyter and Gaudron, Methods in Molecular Biology, Vol. 74, Chapter 43, “Expressing Ribozymes in Plants”, Edited by Turner, P. C., Humana Press Inc., Totowa, N.J. RNA endoribonucleases which have been described, such as the one that occurs naturally in Tetrahymena thermophila, can be useful. See, for example, U.S. Pat. Nos. 4,987,071 and 6,423,885.

PTGS, e.g., RNAi, can also be used to inhibit the expression of a gene. For example, a construct can be prepared that includes a sequence that is transcribed into an RNA that can anneal to itself, e.g., a double stranded RNA having a stem-loop structure. In some embodiments, one strand of the stem portion of a double stranded RNA comprises a sequence that is similar or identical to the sense coding sequence, or a fragment thereof, of the polypeptide of interest, and that is from about 10 nucleotides to about 2,500 nucleotides in length. The length of the sequence that is similar or identical to the sense coding sequence can be from 10 nucleotides to 500 nucleotides, from 15 nucleotides to 300 nucleotides, from 20 nucleotides to 100 nucleotides, or from 25 nucleotides to 100 nucleotides. The other strand of the stem portion of a double stranded RNA comprises a sequence that is similar or identical to the antisense strand, or a fragment thereof, of the coding sequence of the polypeptide of interest, and can have a length that is shorter, the same as, or longer than the corresponding length of the sense sequence. In some cases, one strand of the stem portion of a double stranded RNA comprises a sequence that is similar or identical to the 3′ or 5′ untranslated region, or a fragment thereof, of the mRNA encoding the polypeptide of interest, and the other strand of the stem portion of the double stranded RNA comprises a sequence that is similar or identical to the sequence that is complementary to the 3′ or 5′ untranslated region, respectively, or a fragment thereof, of the mRNA encoding the polypeptide of interest. In other embodiments, one strand of the stem portion of a double stranded RNA comprises a sequence that is similar or identical to the sequence of an intron or a fragment thereof in the pre-mRNA encoding the polypeptide of interest, and the other strand of the stem portion comprises a sequence that is similar or identical to the sequence that is complementary to the sequence of the intron or fragment thereof in the pre-mRNA.

The loop portion of a double stranded RNA can be from 3 nucleotides to 5,000 nucleotides, e.g., from 3 nucleotides to 25 nucleotides, from 15 nucleotides to 1,000 nucleotides, from 20 nucleotides to 500 nucleotides, or from 25 nucleotides to 200 nucleotides. The loop portion of the RNA can include an intron or a fragment thereof. A double stranded RNA can have zero, one, two, three, four, five, six, seven, eight, nine, ten, or more stem-loop structures.

A construct including a sequence that is operably linked to a regulatory region and a transcription termination sequence, and that is transcribed into an RNA that can form a double stranded RNA, is transformed into plants as described below. Methods for using RNAi to inhibit the expression of a gene are known to those of skill in the art. See, e.g., U.S. Pat. Nos. 5,034,323; 6,326,527; 6,452,067; 6,573,099; 6,753,139; and 6,777,588. See also WO 97/01952; WO 98/53083; WO 99/32619; WO 98/36083; and U.S. Patent Publications 20030175965, 20030175783, 20040214330, and 20030180945.

Constructs containing regulatory regions operably linked to nucleic acid molecules in sense orientation can also be used to inhibit the expression of a gene. The transcription product can be similar or identical to the sense coding sequence of a polypeptide of interest. The transcription product can also be unpolyadenylated, lack a 5′ cap structure, or contain an unsplicable intron. Methods of inhibiting gene expression using a full-length cDNA as well as a partial cDNA sequence are known in the art. See, e.g., U.S. Pat. No. 5,231,020.

In some embodiments, a construct containing a nucleic acid having at least one strand that is a template for both sense and antisense sequences that are complementary to each other is used to inhibit the expression of a gene. The sense and antisense sequences can be part of a larger nucleic acid molecule or can be part of separate nucleic acid molecules having sequences that are not complementary. The sense or antisense sequence can be a sequence that is identical or complementary to the sequence of an mRNA, the 3′ or 5′ untranslated region of an mRNA, or an intron in a pre-mRNA encoding a polypeptide of interest, or a fragment of such sequences. In some embodiments, the sense or antisense sequence is identical or complementary to a sequence of the regulatory region that drives transcription of the gene encoding a polypeptide of interest. In each case, the sense sequence is the sequence that is complementary to the antisense sequence.

The sense and antisense sequences can be any length greater than about 12 nucleotides (e.g., 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or more nucleotides). For example, an antisense sequence can be 21 or 22 nucleotides in length. Typically, the sense and antisense sequences range in length from about 15 nucleotides to about 30 nucleotides, e.g., from about 18 nucleotides to about 28 nucleotides, or from about 21 nucleotides to about 25 nucleotides.

In some embodiments, an antisense sequence is a sequence complementary to an mRNA sequence encoding a lignin-modulating polypeptide set forth in SEQ ID NO:96, SEQ ID NOs:98-107, SEQ ID NOs:109-111, SEQ ID NOs:113-114, SEQ ID NOs:116-124, SEQ ID NOs:126-127, SEQ ID NOs:129-130, SEQ ID NO:132, SEQ ID NO:134, SEQ ID NO:136, SEQ ID NO:138, SEQ ID NO:140, SEQ ID NOs:142-143, SEQ ID NOs:145-147, SEQ ID NOs:149-150, SEQ ID NOs:152-156, SEQ ID NO:158, SEQ ID NOs:160-163, SEQ ID NO:165, SEQ ID NOs:167-174, SEQ ID NOs:176-181, SEQ ID NO:183, SEQ ID NO:185, SEQ ID NOs:187-188, SEQ ID NO:190, SEQ ID NOs:192-194, SEQ ID NOs:196-197, SEQ ID NO:199, SEQ ID NOs:201-202, SEQ ID NO:204, SEQ ID NO:206, SEQ ID NO:208, SEQ ID NOs:210-214, SEQ ID NO:216, SEQ ID NOs:218-220, SEQ ID NO:222, SEQ ID NO:224, SEQ ID NOs:226-227, SEQ ID NO:229, SEQ ID NO:231, SEQ ID NOs:233-238, SEQ ID NO:240, SEQ ID NO:242, SEQ ID NO:244, SEQ ID NO:246, SEQ ID NO:248, SEQ ID NO:250, SEQ ID NO:252, SEQ ID NO:254, SEQ ID NOs:256-268, SEQ ID NOs:270-279, SEQ ID NOs:281-282, SEQ ID NO:284, SEQ ID NOs:286-287, SEQ ID NO:289, SEQ ID NOs:291-298, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NOs:304-309, SEQ ID NOs:311-319, SEQ ID NOs:321-330, SEQ ID NOs:332-340, SEQ ID NO:342, SEQ ID NO:344, SEQ ID NOs:355-356, SEQ ID NOs:358-369, SEQ ID NO:371, SEQ ID NOs:373-385, SEQ ID NOs:390-395, SEQ ID NO:397, SEQ ID NO:399, SEQ ID NOs:401-407, SEQ ID NOs:409-463, SEQ ID NOs:465-496, SEQ ID NOs:498-500, SEQ ID NOs:502-503, SEQ ID NO:505, SEQ ID NOs:507-511, SEQ ID NOs:513-540, SEQ ID NO:542, SEQ ID NOs:544-571, SEQ ID NOs:579-581, SEQ ID NOs:583-587, SEQ ID NOs:589-590, SEQ ID NO:592, SEQ ID NOs:595-599, SEQ ID NOs:601-617, SEQ ID NO:619, SEQ ID NOs:621-638, SEQ ID NOs:640-672, SEQ ID NO:674, SEQ ID NOs:676-678, SEQ ID NO:680, SEQ ID NOs:682-685, SEQ ID NO:687, SEQ ID NO:689, SEQ ID NOs:691-714, SEQ ID NOs:716-717, SEQ ID NOs:719-737, SEQ ID NO:739, SEQ ID NOs:741-766, SEQ ID NO:768, SEQ ID NOs:770-776, SEQ ID NO:778, SEQ ID NOs:780-786, SEQ ID NOs:788-792, SEQ ID NO:794-807, or SEQ ID NOs:809-820.

The sense sequence complementary to the antisense sequence can be a sequence present within the mRNA of a lignin-modulating polypeptide. Typically, sense and antisense sequences are designed to correspond to a 15-30 nucleotide sequence of a target mRNA such that the level of that target mRNA is reduced.

In some embodiments, a construct containing a nucleic acid having at least one strand that is a template for more than one sense sequence (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10 or more sense sequences) can be used to inhibit the expression of a gene. Likewise, a construct containing a nucleic acid having at least one strand that is a template for more than one antisense sequence (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10 or more antisense sequences) can be used to inhibit the expression of a gene. For example, a construct can contain a nucleic acid having at least one strand that is a template for two sense sequences and two antisense sequences. The multiple sense sequences can be identical or different, and the multiple antisense sequences can be identical or different. For example, a construct can have a nucleic acid having one strand that is a template for two identical sense sequences and two identical antisense sequences that are complementary to the two identical sense sequences. Alternatively, an isolated nucleic acid can have one strand that is a template for (1) two identical sense sequences 20 nucleotides in length, (2) one antisense sequence that is complementary to the two identical sense sequences 20 nucleotides in length, (3) a sense sequence 30 nucleotides in length, and (4) three identical antisense sequences that are complementary to the sense sequence 30 nucleotides in length. The constructs provided herein can be designed to have any arrangement of sense and antisense sequences. For example, two identical sense sequences can be followed by two identical antisense sequences or can be positioned between two identical antisense sequences.

A nucleic acid having at least one strand that is a template for one or more sense and/or antisense sequences can be operably linked to a regulatory region to drive transcription of an RNA molecule containing the sense and/or antisense sequence(s). In addition, such a nucleic acid can be operably linked to a transcription terminator sequence, such as the terminator of the nopaline synthase (nos) gene. In some cases, two regulatory regions can direct transcription of two transcripts: one from the top strand, and one from the bottom strand. See, for example, Yan et al., Plant Physiol., 141:1508-1518 (2006). The two regulatory regions can be the same or different. The two transcripts can form double-stranded RNA molecules that induce degradation of the target RNA. In some cases, a nucleic acid can be positioned within a T-DNA or P-DNA such that the left and right T-DNA border sequences, or the left and right border-like sequences of the P-DNA, flank or are on either side of the nucleic acid. The nucleic acid sequence between the two regulatory regions can be from about 15 to about 300 nucleotides in length. In some embodiments, the nucleic acid sequence between the two regulatory regions is from about 15 to about 200 nucleotides in length, from about 15 to about 100 nucleotides in length, from about 15 to about 50 nucleotides in length, from about 18 to about 50 nucleotides in length, from about 18 to about 40 nucleotides in length, from about 18 to about 30 nucleotides in length, or from about 18 to about 25 nucleotides in length.

In some nucleic-acid based methods for inhibition of gene expression in plants, a suitable nucleic acid can be a nucleic acid analog. Nucleic acid analogs can be modified at the base moiety, sugar moiety, or phosphate backbone to improve, for example, stability, hybridization, or solubility of the nucleic acid. Modifications at the base moiety include deoxyuridine for deoxythymidine, and 5-methyl-2′-deoxycytidine and 5-bromo-2′-deoxycytidine for deoxycytidine. Modifications of the sugar moiety include modification of the 2′ hydroxyl of the ribose sugar to form 2′-O-methyl or 2′-O-allyl sugars. The deoxyribose phosphate backbone can be modified to produce morpholino nucleic acids, in which each base moiety is linked to a six-membered morpholino ring, or peptide nucleic acids, in which the deoxyphosphate backbone is replaced by a pseudopeptide backbone and the four bases are retained. See, for example, Summerton and Weller, 1997, Antisense Nucleic Acid Drug Dev., 7:187-195; Hyrup et al., Bioorgan. Med. Chem., 4:5-23 (1996). In addition, the deoxyphosphate backbone can be replaced with, for example, a phosphorothioate or phosphorodithioate backbone, a phosphoroamidite, or an alkyl phosphotriester backbone.

Transgenic Plant Cells and Plants

Provided herein are transgenic plant cells and plants comprising at least one recombinant nucleic acid construct or exogenous nucleic acid. A recombinant nucleic acid construct or exogenous nucleic acid can include a regulatory region as described herein, a nucleic acid encoding a lignin-modulating polypeptide as described herein, or both. In certain cases, a transgenic plant cell or plant comprises at least two recombinant nucleic acid constructs or exogenous nucleic acids, e.g., one including a nucleic acid encoding one lignin-modulating polypeptide, and another including a nucleic acid encoding a second lignin-modulating polypeptide.

A plant or plant cell used in methods of the invention contains a recombinant nucleic acid construct as described herein. A plant or plant cell can be transformed by having a construct integrated into its genome, i.e., can be stably transformed. Stably transformed cells typically retain the introduced nucleic acid with each cell division. A plant or plant cell can also be transiently transformed such that the construct is not integrated into its genome. Transiently transformed cells typically lose all or some portion of the introduced nucleic acid construct with each cell division such that the introduced nucleic acid cannot be detected in daughter cells after a sufficient number of cell divisions. Both transiently transformed and stably transformed transgenic plants and plant cells can be useful in the methods described herein.

Typically, transgenic plant cells used in methods described herein constitute part or all of a whole plant. Such plants can be grown in a manner suitable for the species under consideration, either in a growth chamber, a greenhouse, or in a field. Transgenic plants can be bred as desired for a particular purpose, e.g., to introduce a recombinant nucleic acid into other lines, to transfer a recombinant nucleic acid to other species or for further selection of other desirable traits. Alternatively, transgenic plants can be propagated vegetatively for those species amenable to such techniques. Progeny includes descendants of a particular plant or plant line provided the progeny inherits the transgene. Progeny of an instant plant include seeds formed on F₁, F₂, F₃, F₄, F₅, F₆ and subsequent generation plants, or seeds formed on BC₁, BC₂, BC₃, and subsequent generation plants, or seeds formed on F₁BC₁, F₁BC₂, F₁BC₃, and subsequent generation plants. Seeds produced by a transgenic plant can be grown and then selfed (or outcrossed and selfed) to obtain seeds homozygous for the nucleic acid construct.

Transgenic plant cells growing in suspension culture, or tissue or organ culture, can be useful for extraction of polypeptides or compounds of interest, e.g., lignin monomers, compounds in a lignin biosynthetic pathway, or flavonoids. For the purposes of this invention, solid and/or liquid tissue culture techniques can be used. When using solid medium, transgenic plant cells can be placed directly onto the medium or can be placed onto a filter film that is then placed in contact with the medium. When using liquid medium, transgenic plant cells can be placed onto a floatation device, e.g., a porous membrane that contacts the liquid medium. Solid medium typically is made from liquid medium by adding agar. For example, a solid medium can be Murashige and Skoog (MS) medium containing agar and a suitable concentration of an auxin, e.g., 2,4-dichlorophenoxyacetic acid (2,4-D), and a suitable concentration of a cytokinin, e.g., kinetin.

When transiently transformed plant cells are used, a reporter sequence encoding a reporter polypeptide having a reporter activity can be included in the transformation procedure and an assay for reporter activity or expression can be performed at a suitable time after transformation. A suitable time for conducting the assay typically is about 1-21 days after transformation, e.g., about 1-14 days, about 1-7 days, or about 1-3 days. The use of transient assays is particularly convenient for rapid analysis in different species, or to confirm expression of a heterologous lignin-modulating polypeptide whose expression has not previously been confirmed in particular recipient cells.

Techniques for introducing nucleic acids into monocotyledonous and dicotyledonous plants are known in the art, and include, without limitation, Agrobacterium-mediated transformation, viral vector-mediated transformation, electroporation and particle gun transformation, e.g., U.S. Pat. Nos. 5,538,880, 5,204,253, 6,329,571 and 6,013,863. If a cell or tissue culture is used as the recipient tissue for transformation, plants can be regenerated from transformed cultures if desired, by techniques known to those skilled in the art. See, e.g., Niu et al., Plant Cell Rep. V19:304-310 (2000); Chang and Yang, Bot. Bull. Acad. Sin., V37:35-40 (1996), and Han et al., Biotechnology in Agriculture and Forestry, V44:291 (ed. by Y. P. S. Bajaj), Springer-Vernag, (1999).

A population of transgenic plants can be screened and/or selected for those members of the population that have a desired trait or phenotype conferred by expression of the transgene. Selection and/or screening can be carried out over one or more generations, which can be useful to identify those plants that have a desired trait, such as an increased lignin content. Selection and/or screening can also be carried out in more than one geographic location. In some cases, transgenic plants can be grown and selected under conditions which induce a desired phenotype or are otherwise necessary to produce a desired phenotype in a transgenic plant. In addition, selection and/or screening can be carried out during a particular developmental stage in which the phenotype is exhibited by the plant.

Plant Species

The polynucleotides and vectors described herein can be used to transform a number of monocotyledonous and dicotyledonous plants and plant cell systems, including dicots such as alfalfa, ash, beech, birch, canola, cherry, clover, cotton, cottonseed, eucalyptus, flax, jatropha, mahogany, maple, mustard, oak, poplar, oilseed rape, rapeseed (high erucic acid and canola), red clover, teak, tomato, walnut, and willow, as well as monocots such as barley, bluegrass, canarygrass, corn, fescue, field corn, millet, miscanthus, oat, rice, rye, ryegrass, sorghum, sudangrass, sugarcane, sweet corn, switchgrass, turf grasses, timothy, and wheat. Gymnosperms such as fir, pine, and spruce can also be suitable.

Thus, the methods and compositions described herein can be used with dicotyledonous plants belonging, for example, to the orders Asterales, Capparales, Euphorbiales, Fabales, Fagales, Juglandales, Lamiales, Linales, Malvales, Myrtales, Rosales, Salicales, Sapindales, Scrophulariales, and Solanales. The methods and compositions described herein also can be utilized with monocotyledonous plants such as those belonging to the order Cyperales, and with plants belonging to Gymnospermae, e.g., Cycadales, Ephedrales, Ginkgoales, Gnetales, and Pinales.

The methods and compositions can be used over a broad range of plant species, including species from the dicot genera Acer, Afzelia, Arabidopsis, Betula, Brassica, Eucalyptus, Fagus, Fraxinus, Glycine, Gossypium, Jatropha, Juglans, Linum, Lycopersicon, Medicago, Micropus, Populus, Prunus, Quercus, Salix, Solanum, Tectona, and Trifolium; and the monocot genera Agrostis, Avena, Festuca, Hordeum, Lemna, Lolium, Milium, Miscanthus, Oryza, Panicum, Pennisetum, Phalaris, Phleum, Poa, Saccharum, Secale, Sorghum, Triticum, Zea, and Zoysia; and the gymnosperm genera Abies, Picea, and Pinus.

In some embodiments, a plant is a member of the species Festuca arundinacea, Miscanthus hybrid (Miscanthus×giganteus), Miscanthus sinensis, Miscanthus sacchariflorus, Panicum virgatum, Pennisetum purpureum, Phalaris arundinacea, Populus balsamifera, Saccharum spp., Secale cereale, Sorghum almum, Sorghum halcapense, or Sorghum vulgare.

In certain embodiments, the polynucleotides and vectors described herein can be used to transform a number of monocotyledonous and dicotyledenous plants and plant cell systems, wherein such plants are hybrids of different species or varieties of a specific (e.g., Saccharum sp.×Miscanthus sp.)

Transgenic Plant Phenotypes

Materials and methods described herein are useful for modulating the amount and/or chemical composition of lignin in plants. For example, a transgenic plant, tissue, or cell comprising a recombinant nucleic acid expressing a lignin-modulating polypeptide can have a modulated amount and/or rate of lignin biosynthesis. Plants, tissues, or cells containing a recombinant nucleic acid construct described herein typically have a difference in the amount, rate of synthesis, and/or chemical composition of lignin, relative to a corresponding control plant, tissue, or cell that is not transformed with the recombinant nucleic acid construct.

A number of different types of lignin, based on chemical and structural features, can be produced by different species of plants, by different tissues of the same plant, or by different parts of the same plant cell. Such lignins include, without limitation, lignins comprising primarily or only coniferyl alcohols such as guaiacyl lignin, lignins comprising primarily or only sinapyl alcohols such as syringyl lignin, lignins comprising primarily or only p-coumaryl alcohols such asp-hydroxyphenyl lignin, and lignins comprising primarily or only coniferyl and sinapyl alcohols such as guaiacyl-syringyl lignin. In addition, other compounds can be incorporated into lignins, including, without limitation, coniferyl/sinapyl p-coumarate, coniferyl/sinapyl p-hydroxybenzoate, coniferyl/sinapyl acetate, ferulate esters, 5-hydroxy-coniferyl alcohol, 3,4-dihydroxy-cinnamyl alcohol, feruloyl amides such as tyramine ferulate, coniferaldehyde/sinapaldehyde, vanillin/syringaldehyde, benzodioxanes, 5-hydroxyguaiacyl, and dihydroconiferyl/dihydro-p-coumaryl alcohol.

Using the methods described herein, the amount and/or rate of synthesis of any type of lignin can be modulated, e.g., increased or decreased, in a transgenic plant, tissue, or cell relative to a control plant, tissue, or cell. In some cases, the amounts of two or more types of lignin (e.g., two, three, four, five, six, seven, eight, nine, ten or even more types of lignin) can be independently modulated relative to a control plant, tissue, or cell.

In some embodiments, the amount of lignin is decreased in transgenic plants, tissues, or cells described herein (e.g., transgenic plants expressing a lignin-modulating polypeptide or an antisense or double-stranded RNA targeted to a lignin-modulating polypeptide as described herein). A decrease ratio can be expressed as the ratio of the lignin in such a transgenic plant, tissue, or cell on a weight basis (e.g., fresh weight basis) as compared to the lignin in a corresponding control plant, tissue, or cell (e.g., a corresponding plant, tissue, or cell that lacks the recombinant nucleic acid encoding the lignin-modulating polypeptide or the antisense or double-stranded RNA targeted to a lignin-modulating polypeptide). The decrease ratio can be from about 0.05 to about 0.90. In certain cases, the ratio can be from about 0.2 to about 0.6, or from about 0.4 to about 0.6, or from about 0.3 to about 0.5, or from about 0.2 to about 0.4.

In some cases, a decrease in the amount of lignin in a transgenic plant expressing a lignin-modulating polypeptide as described herein can be calculated as a percent decrease in the weight of lignin extracted per weight of tissue of the transgenic plant relative to the weight of lignin extracted per weight of tissue of a corresponding control plant. For example, the amount of lignin in a tissue of a transgenic plant provided herein can be decreased by about 1% to about 10%, or about 5% to about 15%, or about 20% to about 50%, or about 25% to about 40%, or about 30% to about 60%, or about 50% to about 75%, or about 75% to about 90% relative to the amount of lignin in a tissue of a corresponding control plant.

The decrease in amount of lignin can be restricted in some embodiments to particular tissues and/or organs, relative to other tissues and/or organs. For example, a transgenic plant can have a decreased amount of lignin in stem tissue relative to leaf tissue. The decreased amount of lignin can be in the cell wall of plant cells such as tracheids, xylem fibres, and sclereids.

An increase in the amount of lignin in a transgenic plant, tissue, or cell expressing a regulatory protein as described herein can be from about 1.02-fold to about 10-fold, about 1.03-fold to about 1.7-fold, or about 1.04-fold to about 1.6-fold, or about 1.05-fold to about 1.7-fold, or about 1.06-fold to about 2.3-fold, or about 1.07-fold to about 2.5-fold, or about 1.08-fold to about 2-fold, or about 1.09-fold to about 2.4-fold, or about 1.1-fold to about 2-fold, or about 1.2-fold to about 3-fold, or about 1.3-fold to about 2.5-fold, or about 1.4-fold to about 3-fold, or about 1.5-fold to about 5-fold, or about 2-fold to about 6-fold, or about 2-fold to about 5-fold, or about 1.5-fold to 7-fold, or about 3-fold to about 4-fold, or about 3-fold to about 7.5-fold, or about 4-fold to about 8-fold, or about 5-fold to about 10-fold higher than the amount in corresponding control plants, tissues, or cells.

In some cases, an increase in the amount of lignin in a transgenic plant described herein can be calculated as a percent increase in the weight of lignin extracted per weight of tissue of the transgenic plant relative to the weight of lignin extracted per weight of tissue of a corresponding control plant. For example, the amount of lignin in a tissue of a transgenic plant provided herein can be increased by about 1% to about 10%, or about 5% to about 15%, or about 20% to about 50%, or about 25% to about 40%, or about 30% to about 60%, or about 50% to about 75%, or about 75% to about 100%, or about 90% to about 150%, or about 50% to about 200%, or about 100% to about 300%, or about 150% to about 500%, or about 200 to about 600%, or about 300% to about 800% relative to the amount of lignin in a tissue of a corresponding control plant.

In some embodiments, the lignin that is increased in a tissue of a transgenic plant described herein is either not produced or is not detectable in a corresponding tissue of a control plant. Thus, in such embodiments, the increase in-lignin is infinitely high. For example, in certain cases, a lignin-modulating polypeptide described herein may activate a biosynthetic pathway in a plant tissue that is not normally activated or operational in a control plant tissue and one or more new types of lignin that were not previously produced in that plant tissue can be produced.

The increase in amount of lignin can be restricted in some embodiments to particular tissues and/or organs, relative to other tissues and/or organs. For example, a transgenic plant can have an increased amount of lignin in stem tissue relative to leaf tissue. The increased amount of lignin can be in the cell wall of plant cells such as tracheids, xylem fibres, and sclereids.

In some embodiments, the amount of lignin in transgenic switchgrass (Panicum virgatum) expressing a regulatory protein or an antisense or double-stranded RNA targeted to a regulatory protein as described herein can be decreased by about 40% to about 75%, or about 45% to about 70%, or about 48% to about 68%, or about 50% to about 66%, or about 53% to about 66%, or about 55% to about 65%, or about 57% to about 71%, or about 50% to about 70%, or about 55% to about 60%, or about 60% to about 65% by weight relative to the amount of lignin in corresponding control switchgrass (e.g., corresponding wild-type switchgrass or switchgrass that lacks the nucleic acid encoding the regulatory protein or the antisense or double-stranded RNA targeted to a regulatory protein). In some cases, the decrease ratio of lignin in transgenic switchgrass described herein as compared to the lignin in corresponding control switchgrass can be from about 0.4 to about 0.8, or about 0.4 to about 0.7, or about 0.45 to about 0.7, or about 0.5 to about 0.66, or about 0.5 to about 0.7, or about 0.5 to about 0.68, or about 0.55 to about 0.7, or about 0.6 to about 0.7, or about 0.53 to about 0.66.

In some embodiments, the amount of lignin in transgenic switchgrass expressing a regulatory protein or an antisense or double-stranded RNA targeted to a regulatory protein as described herein can be increased by about 100% to about 300%, or about 100% to about 275%, or about 125% to about 300%, or about 125% to about 275%, or about 150% to about 275%, or about 150% to about 250%, or about 175% to about 250%, or about 175% to about 225%, or about 100% to about 250%, or about 150% to 300% by weight as compared to the amount of lignin in corresponding control switchgrass. In some cases, an increase in lignin in transgenic switchgrass described herein can be from about 1.2-fold to about 3-fold, or about 1.3-fold to about 2-fold, or about 1.3-fold to about 2.5-fold, or about 1.5-fold to about 2.1-fold, or about 1.25-fold to about 2.75-fold, or about 1.2-fold to about 2.15-fold, or about 1.4-fold to about 2.8-fold, or about 1.5-fold to about 2.5-fold, or about 1.75-fold to about 2.75-fold, or about 1.2-fold to about 1.9-fold relative to corresponding control switchgrass.

The amount of lignin in a plant can be determined by known techniques, e.g., the acid detergent, Klason, acetyl bromide, and permanganate lignin methods. See, for example, Hatfield and Fukushima, Crop Sci., 45:832-839 (2005); and Methods in Lignin Chemistry, Dence and Lin, eds., Springer-Verlag, Berlin, p. 33-61 (1992). Pyrolysis-gas chromatography-mass spectrometry, liquid chromatography-mass spectrometry (LC-MS), or a degradative method, e.g., the DFRC method or thioacidolysis, combined with mass spectrometry also can be used. If desired, the composition and structure of lignin can be characterized by GC-MS, LC-MS, nuclear magnetic resonance spectroscopy, Fourier-transform infrared spectroscopy, and/or other known techniques. In addition, histochemical analysis can be performed to determine the amount and distribution of lignin in a plant. For example, tissue sections can be stained with toluidine blue O (TBO), the Wiesner reagent, or the Maiule reagent. TBO is a metachromatic stain that imparts a turquoise color to lignified cell walls and stains non-lignified cell walls purple. Phloroglucinol stains lignified cells red upon reaction with hydroxycinnamaldehyde groups present in the polymer. The Mäule reagent is a histochemical stain that allows syringyl lignin to be distinguished chromogenically from guaiacyl lignin in situ. A pink or red color can indicate the presence of syringyl units, whereas a light to dark brown color can indicate the presence of guaiacyl units.

A transgenic plant, tissue, or cell expressing a lignin-modulating polypeptide described herein can have a modulated, e.g., increased or decreased, level of one or more compounds in a lignin biosynthesis pathway as compared to a control plant, tissue, or cell not transgenic for the particular lignin-modulating polypeptide. In certain cases, the amount of more than one compound (e.g., two, three, four, five, six, seven, eight, nine, ten or even more compounds) included in a lignin biosynthetic pathway can be modulated relative to a control plant, tissue, or cell that is not transgenic for a lignin-modulating polypeptide described herein. Such a compound can be, for example, a precursor compound, an intermediate compound, or an end product in a lignin biosynthesis pathway.

Compounds in a lignin biosynthesis pathway include, without limitation, phenylalanine, cinnamic acid, p-coumaric acid, p-coumaraldehyde, p-coumaryl alcohol, caffeic acid, ferulic acid, 5-hydroxy-ferulic acid, 5-hydroxy-feruloyl CoA, sinapic acid, sinapoyl CoA, p-coumaroyl CoA, p-coumaroyl shikimic acid, p-coumaroyl quinic acid, caffeoyl shikimic acid, caffeoyl quinic acid, caffeoyl CoA, feruloyl CoA, coniferaldehyde, 5-hydroxy-coniferaldehyde, sinapaldehyde, coniferyl alcohol, 5-hydroxy-coniferyl alcohol, sinapyl alcohol, caffeyl aldehyde, and caffeyl alcohol.

An increase in the amount of one or more compounds in a lignin biosynthesis pathway in transgenic cells or tissues expressing a lignin-modulating polypeptide described herein can be from about 1.2-fold to about 150-fold, about 1.3-fold to about 20-fold, or about 1.2-fold to about 3-fold, or about 1.3-fold to about 2-fold, or about 1.4-fold to about 3-fold, or about 2-fold to about 4-fold, or about 2-fold to about 5-fold, or about 1.5-fold to 7-fold, or about 3-fold to about 4-fold, or about 3-fold to about 7-fold, or about 4-fold to about 8-fold, or about 5-fold to about 10-fold, or about 10-fold to about 15-fold, or about 12-fold to about 18-fold, or about 14-fold to about 22-fold, or about 18-fold to about 30-fold, or about 10-fold to about 100-fold, or about 30-fold to about 100-fold, or about 75-fold to about 130-fold, or about 5-fold to about 50-fold, or about 40-fold to about 150-fold higher than the amount in corresponding control cells or tissues that lack the recombinant nucleic acid encoding the lignin-modulating polypeptide.

In some embodiments, the compound in a lignin biosynthesis pathway that is increased in transgenic cells expressing a lignin-modulating polypeptide described herein is either not produced or is not detectable in a corresponding control cell that lacks the recombinant nucleic acid encoding the lignin-modulating polypeptide. Thus, in such embodiments, the increase in such a compound is infinitely high as compared to corresponding control cells or tissues that lack the recombinant nucleic acid encoding the lignin-modulating polypeptide. For example, in certain cases, a lignin-modulating polypeptide described herein may activate a biosynthetic pathway in a plant that is not normally activated or operational in a control plant, and one or more compounds in a lignin biosynthetic pathway that were not previously produced in that plant species can be produced.

The increase in amount of one or more compounds in a lignin biosynthesis pathway can be restricted in some embodiments to particular tissues and/or organs, relative to other tissues and/or organs. For example, a transgenic plant can have an increased amount of a lignin biosynthesis compound in stem tissue relative to leaf or root tissue.

In some embodiments, the amount of one or more than one compound in a lignin biosynthesis pathway is decreased in transgenic cells expressing a lignin-modulating polypeptide as described herein. A decrease ratio can be expressed as the ratio of the compound in such a transgenic cell on a weight basis (e.g., fresh weight basis) as compared to the compound in a corresponding control cell that lacks the recombinant nucleic acid encoding the lignin-modulating polypeptide. The decrease ratio can be from about 0.05 to about 0.90. In certain cases, the ratio can be from about 0.2 to about 0.6, or from about 0.4 to about 0.6, or from about 0.3 to about 0.5, or from about 0.2 to about 0.4.

In certain embodiments, the compound in a lignin biosynthesis pathway that is decreased in transgenic cells expressing a lignin-modulating polypeptide as described herein is decreased to an undetectable level as compared to the level in corresponding control cells that lack the recombinant nucleic acid encoding the lignin-modulating polypeptide. Thus, in such embodiments, the decrease ratio for such a compound is zero.

The decrease in amount of one or more compounds in a lignin biosynthesis pathway can be restricted in some embodiments to particular tissues and/or organs, relative to other tissues and/or organs. For example, a transgenic plant can have a decreased amount of a compound in stem tissue relative to leaf tissue.

In some embodiments, the amounts of two or more compounds in a lignin biosynthesis pathway are increased and/or decreased, e.g., the amounts of two, three, four, five, six, seven, eight, nine, ten, or more, lignin compounds are independently increased and/or decreased. The amount of a lignin compound can be determined by known techniques, e.g., by extraction of compounds in a lignin biosynthesis pathway from a plant tissue followed by gas chromatography-mass spectrometry (GC-MS) or liquid chromatography-mass spectrometry (LC-MS). If desired, the structure of the lignin compound can be confirmed by GC-MS, LC-MS, nuclear magnetic resonance and/or other known techniques.

In addition to having a modulated amount of lignin and/or a modulated level of one or more than one compound in a lignin biosynthesis pathway, a transgenic plant or cell produced using the materials and methods described herein can produce one or more lignins having an altered structure and/or composition relative to the lignin(s) produced by a corresponding control plant or cell that is not transformed with the recombinant nucleic acid construct. For example, the lignin composition can be altered from essentially 100% guaiacyl units to essentially 100% syringyl units. In some cases, the ratio of syringyl to guaiacyl units incorporated into lignin in a transgenic plant can be modulated relative to the corresponding ratio in a control plant. For example, the ratio of syringyl to guaiacyl units can be increased, e.g., by 1.2-fold, 1.3-fold, 1.4-fold, 1.5-fold, 1.6-fold, 1.7-fold, 1.8-fold, 1.9-fold, 2.0-fold, 2.1-fold, 2.2-fold, 2.3-fold, 2.4-fold, 2.5-fold, 2.6-fold, 2.7-fold, 2.8-fold, 2.9-fold, 3.0-fold, or more than 3.0-fold, in a transgenic plant provided herein as compared to the corresponding ratio in a control plant. In some cases, the ratio of syringyl to guaiacyl units incorporated into lignin in a transgenic plant described herein can be decreased, e.g., by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 60%, 70%, 80%, 90%, 100%, or more than 100%, as compared to the corresponding ratio in a control plant. In some cases, the composition of lignin can be altered in a transgenic plant by having compounds incorporated into lignin that are not normally incorporated into lignin in a wild-type plant. Such compounds can include, without limitation, dihydroconiferyl alcohol, coniferaldehyde, hydroxycinnamaldehydes, and hydroxybenzaldehydes. The composition of lignin in a plant can be determined using well known methods, such as those described herein.

Articles of Manufacture

The materials and methods described herein are useful for modifying biomass characteristics, such as characteristics of biomass renewable energy source plants. A biomass renewable energy source plant is a plant having or producing material (either raw or processed) that comprises stored solar energy that can be converted to fuel. In general terms, such plants comprise dedicated energy crops as well as agricultural and woody plants. Examples of biomass renewable energy source plants include:

switchgrass, elephant grass, giant chinese silver grass, energycane, giant reed (also known as wild cane), miscanthus, tall fescue, bermuda grass, sorghum, napier grass (also known as uganda grass), triticale, rye, winter wheat, shrub poplar, shrub willow, big bluestem, reed canary grass, and corn.

Transgenic plants provided herein have particular uses in agricultural industries. For example, transgenic plants, e.g., trees, described herein can be used to produce wood that is more lignified, and therefore more durable, than wood from corresponding wild-type plants. Such wood can serve as a superior wood fuel and/or raw material for applications such as woodworking. Transgenic plants such as trees having increased lignin content can also serve as sinks for carbon in the biosphere. Increased sequestration of carbon as lignin in transgenic plants may reduce atmospheric carbon dioxide and global warming. Transgenic plants having an increased lignin content can also be used to produce crops that are less susceptible to lodging. Increasing lignin in fruit, such as tomatoes, can increase the firmness of the fruit, thereby making it more amenable to shipping, storing, slicing, and dicing.

Also provided herein are transgenic plants, such as trees, having a reduced lignin content, which can be useful, e.g., to reduce the pulping cost and energy consumption in the pulping process used to make paper from wood. In addition, transgenic plants having a reduced lignin content can produce crops that are more digestible than crops produced from wild-type plants, which, in turn, can impact the livestock industry. Feeding dairy cattle corn silage produced from corn plants having a reduced and altered lignin content due to homozygosity at one or more bm loci can improve milk production (See, U.S. Pat. No. 6,114,609). Plants having a reduced lignin content also can be valuable for the production of biofuels. The crosslinking structure of lignin is known to complex with cellulose and hemicellulose, thus limiting the efficiency of the conversion process to produce ethanol from plant material. Reducing the lignin content in plants may increase the yield of ethanol from the plant material. See, for example, Mooney et al., Bioresour Technol, 64:113-119 (1998); Bernardez et al., Biotechnol Bioeng., 42:899-907 (1993); Chernoglazov et al., Enzyme Microbiol Technol, 10:503-507 (1988); and Vinzant et al., Appl Biochem Biotechnol, 62:99-104 (1997).

Lignin itself, which can be harvested from transgenic plants provided herein, can be converted into valuable fuel additives. Lignin can be removed from wood pulp of transgenic trees having an increased lignin content, and lignin can be recovered from any bioethanol production process using agricultural materials such as straw, corn stalks and switchgrass engineered to have an increased lignin content. Lignin can be combusted to provide heat and/or power for the ethanol process; however, increasing the value of the lignin by converting it to higher value fuel additives can significantly enhance the competitiveness of bioethanol technology. Lignins removed from wood pulp as sulphates can be used as dust suppression agents for roads, as dispersants in high performance cement applications, water treatment formulations, and textile dyes, or as raw materials for several chemicals, such as vanillin, DMSA, ethanol, torula yeast, xylitol sugar, and humic acid.

Seeds of transgenic plants described herein can be conditioned and bagged in packaging material by means known in the art to form an article of manufacture. Packaging material such as paper and cloth are well known in the art. A package of seed can have a label, e.g., a tag or label secured to the packaging material, a label printed on the packaging material, or a label inserted within the package. The package label may indicate that the seed herein incorporates transgenes that provide increased amounts of lignin in one or more tissues of plants grown from such seeds.

The invention will be further described in the following examples, which do not limit the scope of the invention described in the claims.

EXAMPLES Example 1 Histological Analysis of Lignin Content in Transgenic Arabidopsis Lines

Transgenic Arabidopsis lines were analyzed for lignin content using histological staining. Each transgenic line that was analyzed is listed in Table 1 along with identifiers for the corresponding nucleic acid used to transform Arabidopsis plants, the polypeptide encoded by the nucleic acid, and the promoter used to express the polypeptide.

TABLE 1 Transgenic Arabidopsis lines analyzed for lignin content Nucleic Nucleic Nucleic Acid Transgenic Acid Acid SEQ ID Polypeptide Line ID Promoter Clone_ID Annot_ID NO: SEQ ID NO: ME06087 35S 11114 225 226 ME03210 35S 108362 221 222 ME12890 35S 21243 283 284 ME01050 32449 38915 285 286 ME01752 35S 8049 290 291 ME04929 35S 1006105 215 216 ME04199 35S 1014844 217 218 ME04941 35S 114130 239 240 ME01739 35S 41046 288 289 ME18822 35S 860791 148 149 ME18127 35S 869854 191 192 ME13394 35S 867623 175 176 ME17216 35S 858797 133 134 ME20615 35S 870466 195 196 ME05326 35S 535161 97 98 ME05335 35S 535161 97 98 ME11531 35S 837136 125 126 ME17696 35S 868753 182 183 ME07663 13879F 521911 95 96 ME20794 35S 869790 189 190 ME18779 35S 863641 159 160 ME18169 35S 887718 203 204 ME21595 35S 860676 135 136 ME23567 35S 343 344 ME23565 35S 341 342 ME00259 32449 11988 280 281

Seeds from the transgenic lines listed in Table 1 were sown in a 60:40 mixture of Sunshine Mix #5 and coarse vermiculite. The sown seeds were stratified for at least three days in a refrigerated cabinet prior to germination in the greenhouse.

To test the staining protocol and determine the optimum developmental stage for histology screening, wild-type plants were collected at different time points starting from the seedling stage just after bolting, about 16 to 18 days after germination, up to the mature stage, about 35 days after germination. Based on the results of this analysis, which are summarized in Table 2 below, Arabidopsis plants were allowed to grow for at least 24 to 26 days post-germination prior to performing the primary histological analysis.

Some of the transgenic lines were analyzed further for ectopic lignin accumulation. Transgenic Arabidopsis seedlings were collected two weeks post germination and incubated overnight in a 12-well dish containing 80% ethanol to remove the chlorophyll. In addition, mature rosette and cauline leaves were collected from transgenic plants five weeks after germination, placed in a 12-well dish, and processed in a manner similar to the manner in which the seedlings were processed.

Phloroglucinol Staining

For the primary histological analysis, the main inflorescence stem was cut at the basal end, about 0.5 cm from the junction of the rosette leaves, using a razor blade. Thin sections of the stems, about 200 microns thick, were manually generated using a razor blade against a Styrofoam support. Up to three individual plants were sampled from each transformation event. Up to five transformation events per transgenic line were used.

The tissue sections were immediately placed on a microscope slide and a drop of 1% phloroglucinol solution in 6 M HCl was placed on top of each section to adequately cover the sample for about two minutes. The phloroglucinol reagent present in the tissue sections was diluted by adding about five drops of water using a pipette. A cover slip was placed on the tissue sections in preparation for microscopy, and any excess liquid was removed with a tissue paper.

For seedlings and whole leaf tissues, ethanol was removed after overnight incubation and replaced with one mL of 1% phloroglucinol solution in 6 M HCl to cover the tissues in the well. The tissues were stained for about two minutes. The phloroglucinol solution was subsequently removed and replaced with one mL of water. The tissues were kept in the 12-well dish for scanning.

Microscopey, Image Acquisition, and Image Analysis

Digital images of tissue sections were taken in tif format at 50× magnification using a Carl Zeiss Axioshop 2 microscope set in a dark field view at 3200K exposure. The microscope was linked to Axiovision software version 3.1.2.1 set at 3200K white balance exposure. The tif format images were adjusted and converted into jpeg format using the Adobe Photoshop plug-in software (AGD Color Temperature Correction version 4) set at 6000K correction condition.

The adjusted jpeg format images were read by WinRhizo Pro software (Regent Instruments Inc.) using a calibration method to classify the pixels within the image view according to whether they belonged to stained lignified cells/tissues (designated as X), to non-lignified cells/tissues (designated as NL), or to the background (designated as B). The results of this “binning” process were exported into an Excel spreadsheet.

The lignified area within an image taken at 50× magnification was semi-quantified and represented as the ratio (R) of the lignified region relative to the whole tissue within an image. The R value was calculated as follows: R=X/(X+NL). The R values from tissue sections of three plants per transformation event were averaged, and the standard deviation was calculated for each average R value. The average R value and standard deviation for each transformation event was compared to the average R value and standard deviation for the wild-type plants to determine whether the difference between the average R values was statistically significant.

The degree of increase or decrease in lignin content within the sampled stem sections of a transgenic line relative to the lignin content in sampled stem sections of wild-type plants was calculated using the following formula. [(R _(transgenic))−(Average R _(Wild-type))]/(Average R _(Wild-type))×100

A relative value, calculated using the formula above, that was positive indicated an increased lignin content in the transgenic line relative to wild-type plants (Table 3). A relative value that was negative indicated a decreased lignin content in the transgenic line relative to wild-type plants (Table 3).

The microscope images of stem tissue sections were also qualitatively inspected to determine if there was ectopic deposition of lignin in regions not normally lignified in wild-type stem tissues, or if there were developmental changes in tissue arrangement compared to the arrangement in wild-type plants.

Digital images of seedlings and whole leaf tissues were taken in jpeg format using an Epson 4870 Photo Scanner. Images of transgenic tissues were compared to images of wild-type tissues to qualitatively determine if there was ectopic or increased accumulation of lignin in organs from transgenic plants as compared to organs from wild-type plants.

Results of Histological Analysis

Results of the semi-quantitative analysis of the lignified areas of stem sections from wild-type Arabidopsis plants at different developmental stages are summarized in Table 2.

TABLE 2 Lignin content of wild-type Arabidopsis plants at different stages of development Development Stage (Days after Stem R value Standard Germination) Region (Average) Deviation Comments 18 Top N/A Tissues too soft for sectioning Middle 0.03 Tissues still soft for sectioning Base 0.06 Tissues still soft for sectioning 24 Top N/A Tissues too soft for sectioning Middle 0.25 0.04 Base 0.30 0.06 25 Top N/A Tissues too soft for sectioning Middle N/A Base 0.29 0.03 27 Top 0.17 Tissues still soft for sectioning Middle 0.23 0.03 Base 0.32 0.10 35 Top 0.23 0.08 Middle 0.21 0.005 Base 0.37 0.09 Stem becoming brittle

Based on the results presented in Table 2, the basal regions of transgenic and corresponding wild-type control plants between 24 to 26 days post germination were used for histological analysis. The results are summarized in Table 3.

TABLE 3 Summary of the histological analysis of lignin content in transgenic Arabidopsis lines Change in Gemini ID lignin content or relative to Genomic Construct Transgenic line- wild-type Observable Locus Code event controls Phenotype 5217C1¹ 5217C1 ME23567-01 76% Decrease Shorter than wild-type 5217G1¹ 5217G1 ME23565-04 33% Increase Enlarged interfascicular cells towards the epidermis At1g08200 ANNOT ID ME18779-01 14% Decrease Shorter than wild-type 863641 ME18779-05 14% Decrease Shorter than wild-type At1g20190 Clone ID ME03210-02 22% Increase 108362 ME03210-04 35% Increase At1g52880 Clone ID 21243 ME12890-03  9% Increase Shorter than wild-type ME12890-04  9% Increase Shorter than wild-type At1g55330 ANNOT ID ME13394-01  2% Increase 867623 ME13394-03 21% Increase ME13394-04 32% Increase ME13394-05 29% Increase At1g64440 ANNOT ID ME11531-01 24% Increase 837136 ME11531-02 13% Increase ME11531-03 14% Increase ME11531-05  5% Increase Dull green leaves At1g68470 ANNOT ID ME17696-04 12% Increase 868753 ME17696-05 13% Increase At1g74550 ANNOT ID ME07663-11 15% Increase 521911 ME07663-12 12% Increase At1g76790 ANNOT ID ME20794-01 21% Increase 869790 ME20794-02 11% Increase ME20794-03 29% Increase At1g77520 ANNOT ID ME18127-01  4% Increase 869854 ME18127-02 35% Increase ME18127-03 25% Increase ME18127-05 30% Increase At2g04780 Clone ID 11114 ME06087-01 19% Increase ME06087-02 18% Increase At2g16720 Clone ID ME04929-04 33% Increase 1006105 ME04929-09 31% Increase ANNOT ID ME17216-02 14% Increase Early bolting 858797 ME17216-03 24% Increase Early bolting ME17216-05  7% Increase Early bolting At2g30490 Clone ID 41046 ME01739-01 12% Increase ME01739-04  4% Increase ME01739-05 17% Increase At2g32990 ANNOT ID ME21595-03 23% Increase 860676 ME21595-04 20% Increase At2g33590 ANNOT ID ME18822-01 35% Increase 860791 ME18822-02 28% Increase At3g02210 ANNOT ID ME20615-01 14% Increase 870466 ME20615-02 11% Increase At4g34050 Clone ID 8049 ME01752-01 23% Increase ME01752-02 12% Increase ME01752-04 17% Increase At4g36220 ANNOT ID ME05326-03 17% Decrease Shorter than wild-type; 535161 yellow-orange throughout Mäule section (predominantly G lignin) ME05326-05 18% Decrease Shorter than wild-type ME05335-02 17% Decrease Shorter than wild-type At4g38400 Clone ID 38915 ME01050-01 18% Increase Ectopic lignin in seedling petiole ME01050-02 20% Increase Ectopic lignin in seedling petiole ME01050-03 27% Increase Ectopic lignin in seedling petiole At5g42100 Clone ID 11988 ME00259-01 48% Decrease Late bolting; shorter than wild-type ME00259-02 44% Decrease Late bolting; shorter than wild-type ME00259-03 55% Decrease Late bolting; shorter than wild-type ME00259-04 55% Decrease Late bolting; shorter than wild-type ME00259-05 62% Decrease Late bolting; shorter than wild-type ME00259-06 60% Decrease Late bolting; shorter than wild-type At5g47370 Clone ID ME04199-01 15% Decrease 1014844 ME04199-04 20% Decrease At5g48930 Clone ID ME04941-01 13% Decrease Shorter than wild-type 114130 ME04941-03 15% Decrease Shorter than wild-type ME04941-04 17% Decrease Shorter than wild-type At5g65730 ANNOT ID ME18169-01 16% Increase 887718 ME18169-02 18% Increase ME18169-03 21% Increase ¹Nucleotide sequence obtained from Populus balsamifera; all other nucleotide sequences were obtained from Arabidopsis thaliana.

Ectopic deposition of lignin was observed in the seedling petiole in transgenic line ME01050, which exhibited increased lignin accumulation. The transgenic line ME23571 was observed to have an increased accumulation of lignin and a vascular bundle arrangement that was altered from a collateral type to an amphivasal type. A collateral type is typical of a wild-type arrangement, where the phloem cells are surrounded by cortex cells towards the epidermal tissues and by xylem cells towards the pith. In an amphivasal type of arrangement, the phloem tissues are surrounded by xylem cells. It appeared that some of the cortical cells were converted to lignified xylem cells in plants from ME23571.

Some transgenic lines such as ME23567, ME18779, ME05326, ME00259, and ME04941 were observed to have a decreased accumulation of lignin relative to wild-type plants and a reduced height. The transgenic line ME04199 also was observed to have a decreased accumulation of lignin, but did not exhibit a reduced height. The cylindrical band corresponding to the xylem-interfascicular region was thinner in the transgenic lines ME05326 and ME04941 than that which is normally observed in wild-type plants at the time the tissue sections were sampled. Plants from the transgenic lines ME03210, ME01050, ME02171, and ME12975 were observed to have an increased accumulation of lignin and a cylindrical band that was expanded relative to that normally observed in wild-type plants at the time the tissue sections were sampled.

Example 2 Determination of Functional Homolog and/or Ortholog Sequences

A subject sequence was considered a functional homolog or ortholog of a query sequence if the subject and query sequences encoded proteins having a similar function and/or activity. A process known as Reciprocal BLAST (Rivera et al., Proc. Natl. Acad. Sci. USA, 95:6239-6244 (1998)) was used to identify potential functional homolog and/or ortholog sequences from databases consisting of all available public and proprietary peptide sequences, including NR from NCBI and peptide translations from Ceres clones.

Before starting a Reciprocal BLAST process, a specific query polypeptide was searched against all peptides from its source species using BLAST in order to identify polypeptides having BLAST sequence identity of 80% or greater to the query polypeptide and an alignment length of 85% or greater along the shorter sequence in the alignment. The query polypeptide and any of the aforementioned identified polypeptides were designated as a cluster.

The BLASTP version 2.0 program from Washington University at Saint Louis, Mo., USA was used to determine BLAST sequence identity and E-value. The BLASTP version 2.0 program includes the following parameters: 1) an E-value cutoff of 1.0e-5; 2) a word size of 5; and 3) the -postsw option. The BLAST sequence identity was calculated based on the alignment of the first BLAST HSP (High-scoring Segment Pairs) of the identified potential functional homolog and/or ortholog sequence with a specific query polypeptide. The number of identically matched residues in the BLAST HSP is alignment was divided by the HSP length, and then multiplied by 100 to get the BLAST sequence identity. The HSP length typically included gaps in the alignment, but in some cases gaps were excluded.

The main Reciprocal BLAST process consists of two rounds of BLAST searches; forward search and reverse search. In the forward search step, a query polypeptide sequence, “polypeptide A,” from source species SA was BLASTed against all protein sequences from a species of interest. Top hits were determined using an E-value cutoff of 10⁻⁵ and a sequence identity cutoff of 35%. Among the top hits, the sequence having the lowest E-value was designated as the best hit, and considered a potential functional homolog or ortholog. Any other top hit that had a sequence identity of 80% or greater to the best hit or to the original query polypeptide was considered a potential functional homolog or ortholog as well. This process was repeated for all species of interest.

In the reverse search round, the top hits identified in the forward search from all species were BLASTed against all protein sequences from the source species SA. A top hit from the forward search that returned a polypeptide from the aforementioned cluster as its best hit was also considered as a potential functional homolog or ortholog.

Functional homologs and/or orthologs were identified by manual inspection of potential functional homolog and/or ortholog sequences. Representative functional homologs and/or orthologs for SEQ ID NO:98, SEQ ID NO:126, SEQ ID NO:136, SEQ ID NO:149, SEQ ID NO:160, SEQ ID NO:176, SEQ ID NO:183, SEQ ID NO:196, SEQ ID NO:204, SEQ ID NO:218, SEQ ID NO:226, SEQ ID NO:240, SEQ ID NO:286, SEQ ID NO:291, SEQ ID NO:134, SEQ ID NO:190, SEQ ID NO:192, SEQ ID NO:342, SEQ ID NO:344, SEQ ID NO:281, SEQ ID NO:284, and SEQ ID NO:289 are shown in FIGS. 1-22, respectively.

Example 3 Determination of Functional Homologs by Hidden Markov Models

Hidden Markov Models (HMMs) were generated by the program HMMER 2.3.2. To generate each HMM, the default HMMER 2.3.2 program parameters, configured for glocal alignments, were used.

An HMM was generated using the sequences shown in FIG. 1 as input. These sequences were fitted to the model and a representative HMM bit score for each sequence is shown in the Sequence Listing. Additional sequences were fitted to the model, and representative HMM bit scores for any such additional sequences are shown in the Sequence Listing. The results indicate that these additional sequences are functional homologs of SEQ ID NO:98.

The procedure above was repeated and an HMM was generated for each group of sequences shown in FIGS. 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, and 22, using the sequences shown in each Figure as input for that HMM. A representative bit score for each sequence is shown in the Sequence Listing. Additional sequences were fitted to certain HMMs, and representative HMM bit scores for such additional sequences are shown in the Sequence Listing. The results indicate that these additional sequences are functional homologs of the sequences used to generate that HMM.

Example 4 Analysis of Lignin Structure and Content in Transgenic Arabidopsis Lines

Arabidopsis overexpression lines (ME lines) were grown in batches in the greenhouse under long-day condition at 28° C. until senescence stage. Each transformation event corresponding to an overexpression line was planted in several pots (represented as replicates) with each pot randomly distributed in separate flats. The corresponding wild type non-transgenic control for each batch was planted in the same manner. At the senescence stage, stem tissues were divided into three parts (bottom, center, and upper) and were collected separately. Collected tissues were dried in a freeze dryer for at least two days before milling.

Pyrolysis GC-MS was performed on a Py-2020 is pyrolyzer (Frontier Labs, Japan) coupled to a QP2010 GC-MS (Shimadzu, Japan). Finely ground material (2 mm minimum) was weighed out (3 mg) into a deactivated stainless steel cup. Sample was introduced into the pyrolyzer set at 500° C. by gravity. The interface between the pyrolyzer and GC inlet was set at 300° C. Separation of pyrolysates was performed on a GC-column (VF-5MS, 30M×0.25 mm×0.25 um). Helium flow through the pyrolyzer and column was set at 1052 mL/min and 1.0 mL/min respectively. Inlet split ratio was 700:1. Column temperature program was initially set at 70° C. (held for 4 minutes) at a ramp rate of 20° C./min to a final temperature of 350° C. Mass spectral acquisition was at 3333 amu/sec from 50 amu-300 amu after a 4.5 min delay.

The areas of the peaks corresponding to different types of lignin monomers (i.e., H=p-Hydroxyphenyl monomer, G=Guaiacyl monomer, S=Syringyl monomer) and to levoglucosan and furfural (both as cellulose markers) were collected. Total lignin is the sum of all the peaks for H, G, and S monomoers. The ratios shown in Table 4 were normalized relative to total lignin.

Comparisons of overexpression lines were made relative to the wild-type control for each batch. The overexpression of the following clones or genes (as indicated by Annot IDs) leads to relatively higher S/G ratio (generally indicative of a positive parameter that may enhance conversion of biomass to ethanol) as shown by their corresponding ME lines: 38915 (ME01050), 108362 (ME03210), 11988 (ME00259), Annot 869854 (ME18127), and Annot 869790 (ME20794).

The overexpression of the following clones leads to lower cellulose/lignin ratio (indicating either an increase in the absolute amount of lignin or decrease in cellulose) as shown by their corresponding ME lines: 11988 (ME00259) and 8049 (ME01752).

TABLE 4 Amount SEQ H/Total G/Total S/Total of Annot Clone ID Transformation Lignin Lignin Lignin S/G H/G Cellulose/ Batch ID ID NO Events Ratio Ratio Ratio Ratio Ratio Lignin 1 1493072 358 ME23571-01-B 0.11 0.62 0.26 0.42 0.18 1 ME23571-03-A 0.12 0.62 0.25 0.41 0.19 1 535161 98 ME05326-03-B 0.10 0.44 0.45 1.01 0.23 1 ME05326-05-C 0.11 0.46 0.43 0.94 0.25 1 38915 286 ME01050-02-B 0.12 0.61 0.26 0.43 0.19 1 ME01050-03-B 0.11 0.62 0.27 0.44 0.17 1 108362 222 ME03210-02-A 0.11 0.61 0.26 0.43 0.19 1 ME03210-04-A 0.12 0.60 0.26 0.43 0.21 1 WT Control WT 0.10 0.64 0.25 0.39 0.16 3 1493072 358 ME23571-01-A 0.13 0.60 0.27 0.44 0.22 0.11 3 ME23571-03-B 0.13 0.57 0.30 0.53 0.23 0.12 3 ME23571-04-B 0.14 0.59 0.27 0.46 0.23 0.10 3 WT Control WT (WS) 0.15 0.56 0.28 0.50 0.27 0.12 4 11988 281 ME00259-05 0.09 0.70 0.20 0.29 0.13 0.03 4 ME00259-06 0.15 0.61 0.25 0.41 0.24 0.14 4 8049 291 ME01752-01 0.11 0.67 0.22 0.33 0.16 0.11 4 ME01752-04 0.09 0.68 0.22 0.33 0.13 0.05 4 869854 192 ME18127-02 0.15 0.61 0.24 0.40 0.24 0.13 4 ME18127-05- 0.11 0.66 0.23 0.34 0.17 0.09 99 4 869790 190 ME20794-01 0.10 0.70 0.20 0.29 0.14 0.10 4 ME20794-03 0.16 0.61 0.23 0.38 0.26 0.12 4 867623 176 ME13394-04-A 0.10 0.69 0.21 0.31 0.14 0.09 4 ME13394-05-A 0.10 0.68 0.21 0.31 0.15 0.08 4 WT Control WT (WS) 0.10 0.68 0.22 0.32 0.15 0.09 5 11114 226 ME06087-01-A 0.11 0.69 0.20 0.29 0.16 0.11 5 ME06087-02-A 0.11 0.69 0.20 0.29 0.16 0.11 5 WT Control WT (WS) 0.11 0.69 0.20 0.29 0.17 0.12 6 535161 98 ME05335-02-B 0.12 0.62 0.26 0.41 0.19 0.11 6 WT Control WT (WS) 0.12 0.64 0.24 0.38 0.19 0.11

Other Embodiments

It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims. 

1. A method of increasing lignin content in a plant, said method comprising: a) introducing into a plant cell an isolated nucleic acid comprising a regulatory region operably linked to a polynucleotide encoding a lignin-modulating polypeptide comprising an amino acid sequence having 95% or greater sequence identity to the amino acid sequence set forth in SEQ ID NO:149, said polypeptide having a nicotinamide adenine dinucleotide (NAD)-dependent epimerase/dehydratase domain; and b) selecting a plant produced from said plant cell that has at least a 35% increase in lignin content in a tissue of the plant as compared to the lignin content in tissue of a corresponding control plant that does not comprise said nucleic acid.
 2. The method of claim 1, wherein said plant cell is capable of producing one or more lignin monomers.
 3. The method of claim 1, wherein said plant is from a genus selected from the group consisting of Agrostis, Avena, Festuca, Hordeum, Lolium, Medicago, Milium, Miscanthus, Panicum, Poa, Saccharum, Sorghum, Trifolium, Triticum, and Zea.
 4. The method of claim 1, wherein said plant is a species selected from the group consisting of: a Miscanthus×giganteus hybrid, Miscanthus sinensis, Miscanthus sacchariflorus, Panicum virgatum, Populus balsamifera, Sorghum almum, Sorghum halepense, Sorghum vulgare, and Saccharum spp.
 5. The method of claim 1, wherein said regulatory region is a promoter.
 6. The method of claim 5, wherein said promoter is a lignin or cellulose biosynthesis promoter.
 7. The method of claim 6, wherein said promoter is selected from the group consisting of SEQ ID NOs:345-354.
 8. The method of claim 5, wherein said promoter is a tissue-preferential promoter.
 9. The method of claim 8, wherein said tissue is secondary cell wall, vascular, stem, pith, xylem, phloem, root, tuber, or leaf tissue.
 10. The method of claim 5, wherein said promoter is a cell type-preferential promoter.
 11. The method of claim 10, wherein said cell is a sieve, laticifer, companion, sclerenchyma, or xylem cell.
 12. The method of claim 5, wherein said promoter is an inducible promoter.
 13. The method of claim 1, wherein said plant is from a genus selected from the group consisting of Eucalyptus, Oryza, Pinus, Populus, Prunus, and Quercus.
 14. The method of claim 1, wherein said method further comprises introducing into said plant cell a nucleic acid encoding a second lignin-modulating polypeptide operably linked to a second regulatory region.
 15. The method of claim 14, wherein said nucleic acid encoding a second lignin-modulating polypeptide operably linked to a second regulatory region is present on a second recombinant nucleic acid construct.
 16. A plant produced by the method of claim
 1. 17. Progeny of the plant of claim 16, wherein said progeny comprises the polynucleotide encoding the lignin-modulating polypeptide comprising an amino acid sequence having 95% or greater identity to the amino acid sequence set forth in SEQ ID NO: 149, said polypeptide having a NAD-dependent epimerase/dehydratase domain, and wherein tissue of said progeny has at least a 35% increase in lignin content as compared to the lignin content in tissue of a corresponding control plant that does not comprise said nucleic acid.
 18. The progeny of claim 17, wherein said progeny is from a genus selected from the group consisting of Agrostis, Avena, Festuca, Hordeum, Lolium, Medicago, Milium, Miscanthus, Panicum, Poa, Saccharum, Sorghum, Trifolium, Triticum, and Zea.
 19. The progeny of claim 18, wherein said progeny is a species selected from the group consisting of: a Miscanthus×giganteus hybrid, Miscanthus sinensis, Miscanthus sacchariflorus, Panicum virgatum, Populus balsamifera, Sorghum almum, Sorghum halepense, Sorghum vulgare, and Saccharum spp. 